Community Intelligence in Knowledge Curation: An Application to Managing Scientific Nomenclature

Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical importance, not only for communications and collaborations with English-speaking people, but also for knowledge dissemination among people in the non-English-speaking world, particularly young students and researchers. However, it lacks of accuracy and standardization when translating scientific nomenclature from English to other languages, especially for those languages that do not belong to the same language family as English. To address this issue, here we propose for the first time the application of community intelligence in scientific nomenclature management, namely, harnessing collective intelligence for translation of scientific nomenclature from English to other languages. As community intelligence applied to knowledge curation is primarily aided by wiki and Chinese is the native language for about one-fifth of the world’s population, we put the proposed application into practice, by developing a wiki-based English-to-Chinese Scientific Nomenclature Dictionary (ESND; http://esnd.big.ac.cn). ESND is a wiki-based, publicly editable and open-content platform, exploiting the whole power of the scientific community in collectively and collaboratively managing scientific nomenclature. Based on community curation, ESND is capable of achieving accurate, standard, and comprehensive scientific nomenclature, demonstrating a valuable application of community intelligence in knowledge curation.     

Costs and Benefits of Chemical Defence in the Red Alga Bonnemaisonia hamifera

A number of studies have shown that the production of chemical defences is costly in terrestrial vascular plants. However, these studies do not necessarily reflect the costs of defence production in macroalgae, due to structural and functional differences between vascular plants and macroalgae. Using a specific culturing technique, we experimentally manipulated the defence production in the red alga Bonnemaisonia hamifera to examine if the defence is costly in terms of growth. Furthermore, we tested if the defence provides fitness benefits by reducing harmful bacterial colonisation of the alga. Costly defences should provide benefits to the producer in order to be maintained in natural populations, but such benefits through protection against harmful bacterial colonisation have rarely been documented in macroalgae. We found that algae with experimentally impaired defence production, but with an externally controlled epibacterial load, grew significantly better than algae with normal defence production. We also found that undefended algae exposed to a natural epibacterial load experienced a substantial reduction in growth and a 6-fold increase in cell bleaching, compared to controls. Thus, this study provides experimental evidence that chemical defence production in macroalgae is costly, but that the cost is outweighed by fitness benefits provided through protection against harmful bacterial colonisation.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

Algicidal Activity of Thiazolidinedione Derivatives Against Harmful Algal Blooming Species

Thiazolidinedione (TD) derivatives exhibit algicidal activity against harmful algal blooming species such as Chattonella marina, Heterosigma akashiwo, and Cochlodinium polykrikoides, as reported previously. In this study, the efficacies and selectivities of TD derivatives were tested by analyzing the structure–activity relationships of various TD derivatives. To investigate structure–activity relationships for growth inhibition of harmful algae, we added a methylene group between the cyclohexyl ring and oxygen of 5-(3-chloro-4-hydroxybenzylidene)-TD, which decreased the inhibitory potency of compound 17. Interestingly, another addition of a methylene group significantly increased the inhibitory potency against C. polykrikoides. The addition of 1 μM compound 17 resulted in the cell rupture of harmful algae after less than 10 h incubation at 20 °C. Compound 17 was applied to both harmful and non-harmful algae and showed a drastic reduction in the efficiency of photosystem II, resulting in reduced photosynthetic oxygen evolution. Compound 17 at a 5 μM concentration destroyed all of the harmful algae, while algicidal activity against non-harmful algae did not exceed 30% of the control within the concentration range tested. In contrast, a herbicide, 3-(3,4-dichlorophenyl)-1,1-dimethylurea, tested at a 5 μM concentration, exhibited 40–70% algicidal activity relative to that of the control against both harmful and non-harmful algae. Compound 17 is a promising lead compound for the development of algicides to control harmful algal blooming species.     

Lithophytic algae: A major threat to the karst formation of show caves

Depending on the intensity, quality and duration ofthe illumination, necessary for viewing show caves,conditions conducive for algal growth are created. Although algae are the major component of this flora,ferns and mosses have also been recorded. Little isknown of the algae, except that they are considered anuisance in terms of discoloration and damage to thekarst formations. The occurrence and possible controlof the algal flora has been studied in the CangoCaves, one of the most important touristic sites inSouth Africa. The algal flora is sparse in speciesdiversity and primitive forms are present. They haveparticular physiological adaptations and usingmicro-oxygen liberation and fluorescence measurements,their photosynthetic characteristics were established. Environmentally friendly control measures wereinvestigated and a solution for their control is proposed.     

A Framework to Report the Production of Renewable Diesel from Algae

Recently, algae have received significant interest as a potential feedstock for renewable diesel (such as biodiesel), and many researchers have attempted to quantify this potential. Some of these attempts are less useful because they have not incorporated specific values of algal lipid content, have not included processing inefficiencies, or omitted processing steps required for renewable diesel production. Furthermore, the associated energy, materials, and costs requirements are sometimes omitted. The accuracy and applicability of these estimates can be improved by using data that are more specific, including all relevant information for renewable diesel production, and by presenting information with more relevant metrics. To determine whether algae are a viable source for renewable diesel, three questions that must be answered are (1) how much renewable diesel can be produced from algae, (2) what is the financial cost of production, and (3) what is the energy ratio of production? To help accurately answer these questions, we propose an analytical framework and associated nomenclature system for characterizing renewable diesel production from algae. The three production pathways discussed in this study are the transesterification of extracted algal lipids, thermochemical conversion of algal biomass, and conversion of secreted algal oils. The nomenclature system is initially presented from a top-level perspective that is applicable to all production pathways for renewable diesel from algae. Then, the nomenclature is expanded to characterize the production of renewable diesel (specifically, biodiesel) from extracted algal lipids in detail (cf. Appendix 2). The analytical framework uses the presented nomenclature system and includes three main principles: using appropriate reporting metrics, using symbolic notation to represent unknown values, and presenting results that are specific to algal species, growth conditions, and product composition.     

A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain

A low-density oligonucleotide array approach based on the hybridization of consensus PCR products of LSU rDNA was developed in order to simultaneously detect various harmful algae. A set of oligonucleotide probes for the hybridization of specific LSU rDNA D2 regions was developed for the identification of 10 representative harmful microalgae. Each probe was spotted onto a streptoavidin-coated glass slide by pipetting. Universal primers were designed within the conserved regions adjacent to the D2 regions of all harmful algae and used to PCR amplify the complete D2 regions. The PCR products were hybridized to the oligonucleotides arrayed on the slide. The array produced unique hybridization patterns for each species of harmful algae and allowed us to differentiate the closely related species. Furthermore, we were able to simultaneously detect several predominant HAB species from a mixture of culture strains and from a natural sample. These results show that DNA microarray can be a new technical platform for parallel discrimination of harmful algae and has great potential to alter the manner in which researchers monitor these microorganisms.     

Development and adaptation of a multiprobe biosensor for the use in a semi-automated device for the detection of toxic algae

Worldwide monitoring programs have been launched for the observation of phytoplankton composition and especially for harmful and toxic microalgae. Several molecular methods are currently used for the identification of phytoplankton but usually require transportation of samples to specialised laboratories. For the purpose of the monitoring of toxic algae, a multiprobe chip and a semi-automated rRNA biosensor for the in-situ detection of toxic algae were developed. Different materials for the electrodes and the carrier material were tested using single-electrode sensors and sandwich hybridisation that is based on species-specific rRNA probes. Phytoplankton communities consist of different species and therefore a biosensor consisting of a multiprobe chip with an array of 16 gold electrodes for the simultaneous detection of up to 14 target species was developed. The detection of the toxic algae is based on a sandwich hybridisation and an electrochemical detection method.     

Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor

The steady rise of observations of harmful or toxic algal blooms throughout the world in the past decades constitute a menace for coastal ecosystems and human interests. As a consequence, a number of programs have been launched to monitor the occurrence of harmful and toxic algae. However, the identification is currently done by microscopic examination, which requires a broad taxonomic knowledge, expensive equipment and is very time consuming. In order to facilitate the identification of toxic algae, an inexpensive and easy-to-handle DNA-biosensor has been adapted for the electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii. The detection of the toxic algae is based on a sandwich hybridisation, which is carried out on a disposable sensor chip. A set of two probes for the species-specific identification of A. ostenfeldii was developed. The specificity of the probes could be shown in dot-blot hybridisations and with the DNA-biosensor. The sensitivity of the DNA-biosensor was optimised with respect to hybridisation temperature and NaCl-concentration and a significant increase of the sensitivity of the DNA-biosensor could be obtained by a fragmentation of the rRNA prior to the hybridisation and by adding a helper oligonucleotide, which binds in close proximity to the probes to the hybridisation.     

Editor's column: Nemagraptus, Pelekysgnathus, Foramenella

Systematic nomenclature follows the same rules for compounding and derivation as the scientific terminology discussed in a preceding Editor's Column. Lethaia honours appealing and correctly constructed names (and terms), but the codes of biological nomenclature do not in practice permit 'justified emendations' of names which do not meet the linguistic requirements in the same codes - in practice priority in 'spelling' supersedes correctness in 'language'. Construction of systematic names is easy, and the introduction of further incorrect and mnemonically cumbersome forms is easily curbed by requiring a statement on the derivation of each new name, scrutinized by a linguist if necessary.     

苦苣苔科植物学名种加词的问题

苦苣苔科植物是个研究活跃的类群,近年来随着新类群的报道和分类系统的变动,在该科的分类学研究中,出现了不少学名的种加词的性和属名不一致或出现拼写错误的情况,虽然这些错误不影响该名称的合格发表,但还是有必要根据《国际藻类、菌物和植物命名法规》进行改正。该文就苦苣苔科植物中属名以-stigma结尾的学名、属名以-cheilos结尾的学名、根据属名词尾不容易判断出性别的学名、拼写错误的名称等问题进行了分析,并对13个不符合法规的名称予以改正。此外,还就苦苣苔科植物学名的合格发表和规范使用进行了讨论。     

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).     

Biological nomenclature terms for facilitating communication in the naming of organisms

A set of terms recommended for use in facilitating communication in biological nomenclature is presented as a table showing broadly equivalent terms used in the traditional Codes of nomenclature. These terms are intended to help those engaged in naming across organism groups, and are the result of the work of the International Committee on Bionomenclature, whose aim is to promote harmonisation and communication amongst those naming life on Earth.     

Some changes in the flora and vegetation of algae in freshwater environments

Changes in the flora and vegetation of algae are discussed with regard to the following aspects: (1) Changes in the distribution of an individual taxon (new colonizations and extinctions); (2) Changes within one group of algae over some decades (examples: desmids of two nature reserves between 1925 and 1980, and charophytes in the region of Berlin since 1800) or over longer periods of time (for example: analysis of diatom frustules in lake sediments since the glacial periods); (3) Changes in the algal flora within a region (for example: the phytoplankton of a small lake in Berlin in 1909 in connection with the restoration of this lake by R. Kolkwitz as compared with the phytoplankton in 1983, or the attempt to show the development in the algal flora in Berlin (West) by a survey of all data available and by planned investigations). — The interpretation of these data often proves difficult due to the problems regarding nomenclature, taxonomy and determination as well as the discontinuity in research, and the different methods applied. Finally, the importance of old reports and the need for modern research are emphasized. “Red Lists” of algae point to the urgent necessity of maintaining as many natural ecosystems as possible.     

香菇的学名及其在当代真菌分类中的位置

本文综述了香菇(Lentinula edodes)的分类历史,确认其在蘑菇目(Agaricales)Tricholomataceae科下的分类地位,并证实了它与多孔菌目(Poriales)Lentinaceae科的Lentinus属没有联系。根据《真菌、地衣汉语学名命名法规》,作者讨论了译为“香菇属”的Lentinus和“小香菇属”的Lentinellus两属的汉语学名问题,提出Lentinus的汉语学名应订正为“韧伞属”,Lentinellus为“螺壳菌属”。香菇所在的Lentinula属的汉语学名建议为“木菇属”。     

Is the Neotropical flora ready for the PhyloCode?

Nomenclatural systems are structured around classification, and together they enable increasingly informed communication about biological diversity. Challengers of Linnaean classification and nomenclature have proposed the PhyloCode, a new set of rules that would govern the way systematists classify and name the diversity of life. Monographs and floras are two fundamental vehicles for communicating information about plant diversity. These works provide a comprehensive foundation of botanical research upon which other scientific studies are based. Information conveyed by monographs and floras is utilized directly or indirectly both within and outside the scientific arena by a wide range of consumers, such as educators, agronomists, ecologists, conservationists, amateur naturalists, and even lawmakers, to name a few. Both classification and nomenclature are essential to the process of synthesis that leads to monographic and floristic treatments and the communication that they facilitate. Conversion to a new system would have far-reaching consequences for the flow of information from systematics to other scientific disciplines, and to society. The purposes of this article are to address the proposed conversion from the perspective of monographic and floristic research focused on Neotropical plant diversity and to point out some difficulties in applying the PhyloCode to the Neotropical flora. Although we welcome improvements in the current nomenclatural system, we conclude that the PhyloCode is not prepared to replace the Linnaean system as a new way to communicate information about Neotropical plant diversity.     

The success (or not) of HUGO nomenclature

Current usage of gene nomenclature is ambiguous and impairs the efficient handling of scientific information. Therefore it is important to propose guidelines to deal with this problem. This study attempts to evaluate the success of HUGO nomenclature for human genes. The results indicate that HUGO guidelines are not supported by the scientific community.     

Stems,nodes, crown clades,and rank‐free lists: is Linnaeus dead?

Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications, and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings, Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have gained strong support among some vocal theoreticians, and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In pratice, phylogenetic nomenclature will bc disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phlylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.     

Molecular approaches to diagnosing nutritional physiology in harmful algae: Implications for studying the effects of eutrophication

Every year harmful algal blooms (HABs) cause serious impacts to local economies, coastal ecosystems, and human health on a global scale. It is well known that nutrient availability can influence important aspects of harmful algae biology and ecology, such as growth, toxin production, and life cycle stage, as well as bloom initiation, persistence and decline. Increases in the rate of supply of organic matter to ecosystems (eutrophication) carries many possible ramifications to coastal systems, including the potential for nutrient enrichment and the potential for stimulation of harmful algal blooms. Traditional studies on algal nutrition typically use either cultured isolates or community level assays, to examine nutrient uptake, nutrient preference, elemental composition, and other metrics of a species’ response to nutrients. In the last decade, technological advances have led to a great increase in the number of sequences available for critical harmful species. This, in turn, has led to new insights with regards to algal nutrition, and these advances highlight the promise of molecular technologies, and genomic approaches, to improving our understanding of algal nutrient acquisition and nutritional physiological ecology, in both cultures and field populations. With these developments increased monitoring of nutritional physiology in field populations of harmful algae will allow us to better discriminate how eutrophication impacts these groups.     

长江口邻近海域赤潮发生区基本特征初探

对长江口邻近海域与赤潮的发生有密切关系、可能影响赤潮生物的生长、迁移、聚集、休眠以及竞争等的一些主要环境特征,如流系结构和水团、冲淡水及其转向、上升流、锋面、营养盐的输入及其来源、浮游生物群落特征等进行了综述,对该海域赤潮发生的历史记录从时间、地点、赤潮类型等方面作了归纳分析,并对2002年在该赤潮发生区开展的现场调查的初步结果作一简略介绍．