A uniform system for microRNA annotation

MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for the identification and annotation of new miRNAs from diverse organisms, particularly so that miRNAs can be reliably distinguished from other RNAs such as small interfering RNAs. We describe specific criteria for the experimental verification of miRNAs, and conventions for naming miRNAs and miRNA genes. Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families.     

A new and unified nomenclature for male fertility restorer (RF) proteins in higher plants

The male fertility restorer (RF) proteins belong to extended protein families associated with the cytoplasmic male sterility in higher plants. Up till now, there is no devised nomenclature for naming the RF proteins. The systematic sequencing of new plant species in recent years has uncovered the existence of several novel RF genes and their encoded proteins. Their naming has been simply arbitrary and could not be adequately handled in the context of comparative functional genomics. We propose in this study a unified nomenclature for the RF extended protein families across all plant species. This new and unified nomenclature relies upon previously developed nomenclature for the first ever characterized RF gene, RF2A/ALDH2B2, a member of ALDH gene superfamily, and adheres to the guidelines issued by the ALDH Genome Nomenclature Committees. The proposed nomenclature reveals that RF gene superfamily encodes currently members of 51 families. This unified nomenclature accommodates functional RF genes and pseudogenes, and offers the flexibility needed to incorporate additional RFs as they become available in future. In addition, we provide a phylogenetic relationship between the RF extended families and use computational protein modeling to demonstrate the high divergence of RF functional specializations through specific structural features of selected members of RF superfamily.     

Minireview: Nomenclature and Classification of Transmitter Receptors: an Integrated Approach

Abstract

This short assay is an attempt to rationalize an integrated approach to transmitter receptor nomenclature and classification based on three criteria: structural information (gene structure/amino acid sequence), operational¹ information (pharmacological/ ligand-defined/recognitory) and transductional information (receptor-effector coupling) are proposed to be used when considering the naming of existing or newly discovered receptors. It should be recognized that none of these criteria has primacy and that in an ideal situation, as much information as feasible on these three aspects should be collected before the naming of a receptor can be agreed upon.     

The "street light syndrome", or how protein taxonomy can bias experimental manipulations

In the genomics era, bioinformatic analysis, especially in non‐model species, facilitates the identification and naming of numerous new proteins, the function of which is then inferred through homology searches. Here, we question certain aspects of these approaches. What are the criteria that permit such a determination? What are their limits? Naming is classifying. We review the different criteria that are used to name a protein and discuss their constraints. We observe that the name given to a protein often introduces a bias for further functional analyses, a bias that is not often taken into account when analysing results. Last but not least, the heterogeneity of criteria used for naming proteins leads to self‐inconsistent or contradictory protein classification that is potentially misleading. Finally, we recommend a wider use of phylogenetic criteria in protein naming. BioEssays 30:349–357, 2008. © 2008 Wiley Periodicals, Inc.     

LISTA, a comprehensive compilation of nucleotide sequences encoding proteins from the yeast Saccharomyces.

The amount of nucleotide sequence data is increasing exponentially. We therefore made an effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. Each sequence has been attributed a single genetic name and in the case of allelic duplicated sequences, synonyms are given, if necessary. For the nomenclature we have introduced a standard principle for naming gene sequences based on priority rules. We have also applied a simple method to distinguish duplicated sequences of one and the same gene from non-allelic sequences of duplicated genes. By using these principles we have sorted out a lot of confusion in the literature and databanks. Along with the genetic name, the mnemonic from the EMBL databank, the codon bias, reference of the publication of the sequence and the EMBL accession numbers are included in each entry.     

The Brain Network of Naming: A Lesson from Primary Progressive Aphasia

Objective

Word finding depends on the processing of semantic and lexical information, and it involves an intermediate level for mapping semantic-to-lexical information which also subserves lexical-to-semantic mapping during word comprehension. However, the brain regions implementing these components are still controversial and have not been clarified via a comprehensive lesion model encompassing the whole range of language-related cortices. Primary progressive aphasia (PPA), for which anomia is thought to be the most common sign, provides such a model, but the exploration of cortical areas impacting naming in its three main variants and the underlying processing mechanisms is still lacking.

Methods

We addressed this double issue, related to language structure and PPA, with thirty patients (11 semantic, 12 logopenic, 7 agrammatic variant) using a picture-naming task and voxel-based morphometry for anatomo-functional correlation. First, we analyzed correlations for each of the three variants to identify the regions impacting naming in PPA and to disentangle the core regions of word finding. We then combined the three variants and correlation analyses for naming (semantic-to-lexical mapping) and single-word comprehension (lexical-to-semantic mapping), predicting an overlap zone corresponding to a bidirectional lexical-semantic hub.

Results and Conclusions

Our results showed that superior portions of the left temporal pole and left posterior temporal cortices impact semantic and lexical naming mechanisms in semantic and logopenic PPA, respectively. In agrammatic PPA naming deficits were rare, and did not correlate with any cortical region. Combined analyses revealed a cortical overlap zone in superior/middle mid-temporal cortices, distinct from the two former regions, impacting bidirectional binding of lexical and semantic information. Altogether, our findings indicate that lexical/semantic word processing depends on an anterior-posterior axis within lateral-temporal cortices, including an anatomically intermediate hub dedicated to lexical-semantic integration. Within this axis our data reveal the underpinnings of anomia in the PPA variants, which is of relevance for both diagnosis and future therapy strategies.     

Formate-dependent growth and homoacetogenic fermentation by a bacterium from human feces: description of Bryantella formatexigens gen. nov., sp. nov

Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at -76 degrees C. 16S rRNA gene sequencing identifies it as a distinct line within the Clostridium coccoides supra-generic rRNA grouping. We propose naming it Bryantella formatexigens gen. nov., sp. nov.     

Proposal for Naming Host Cell-Derived Inserts in Retrovirus Genomes

We propose a system for naming inserted sequences in transforming retroviruses (i.e., onc genes), based on using trivial names derived from a prototype strain of virus.     

A nomenclature for restriction enzymes,DNA methyltransferases,homing endonucleases and their genes

A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.     

中国传统私家园林景点题名中的松柏意象研究

中国传统松柏文化源远流长,蔚为大观。深入挖掘中国古典园林中的松柏文化对于弘扬中国优秀传统文化和提升现代园林文化具有重要意义。现有松柏文化研究主要集中在诗词、绘画、民俗等领域,在园林品题领域的研究还不够系统和深入。以历代私家园林中的景点名称为研究对象,采用古籍文献查询和统计分析相结合的方法,对历代私家园林中的松柏景点、景点题名中的常见意象、松柏景题所表达的精神文化内涵进行研究。结果表明：1）唐代及以前私家园林中的松柏景题记载较少,题名意象也非常单一;2）宋元时期虽然记载的松柏景题仍然不多,但是题名意象已经非常丰富;3）明清时期松柏景题的数量最多,题名意象也最为多元;4）历代私家园林松柏景点除直接以松柏名称题名外,以松风意象题名最多,其次是数量意象、岁寒意象、松阴意象等;5）松柏景题的精神内涵主要表达了历代文人对隐逸理想的寄托、高洁人格的追求、佛理禅思的寓意和对健康长寿的企盼。     

A nomenclature and data model to describe NMR experiments

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Joint first authors     

Phylogenetic analysis and classification of insect achaete-scute complex genes

Achaete-scute complex (ASC) genes play essential roles in neurogenesis of eukaryotes. Insect ASC genes are currently grouped into two distinct families, ASCa and ASCb. However, the identified insect ASCb family genes are not orthologous to known ASCb family genes from other animals such as nematode and mammal. Besides, many ASC genes have been annotated differently in GenBank. In this study, ASC genes from 41 insect species were obtained in silico and analyzed to clarify their evolutionary relationships with known ASC genes from other animals. Based on our analyses, a new naming system is suggested for classification of ASC genes. Firstly, a new family (ASCc) is added into the already existing two families and the gene of this family is named Asl (Achaete-scute-like). Secondly, Ash4, Ash5 and Ash6 are used to name insect ASC genes that are not orthologous to ac, sc, l'sc and ase genes of Drosophila melanogaster and Ash1 to Ash3 genes of Bombyx mori. This naming system can be used to correct inappropriate annotations of insect ASC genes in GenBank and to classify newly identified insect ASC genes. Additionally, a vast difference was found in ASC gene composition among various insect species, suggesting that different insect species might have originated from various ancestral lineages.     

The grapevine gene nomenclature system

Background

Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes.

Results

With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper.

Conclusions

Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.     

Progressive loss of access to spoken word forms in a case of Alzheimer's disease.

We report the results of a longitudinal study of a progressive anomia in a patient with dementia of the Alzheimer type (DAT). The anomia cannot be attributed to a deficit within the semantic system, but appears instead to arise from impaired access to the phonological lexicon at a post-semantic stage of the naming process: a deficit that hitherto has not been reported in DAT. Specific naming responses were affected consistently by the disorder, showing that disorders of access are not invariably associated with inconsistent responding. Before specific responses disappeared from spontaneous use, there appeared to be an intervening stage at which some responses could be elicited by an initial phoneme cue, suggesting a low level of spontaneous activity of insufficient strength to elicit a response unaided. The frequency of the name affected naming performance, but did not appear to interact with the severity of the naming disorder, suggesting that the parameters of the normal naming system were unaffected. It is claimed that important new insights into the characteristics of progressive anomia have been obtained by taking a longitudinal approach.     

White doctors and nurses on racial inequality in health care in the USA: whiteness and colour-blind racial ideology

In this paper we report on an interdisciplinary project interviewing doctors and nurses about racial inequality in health care in the USA. We analysed data from interviews with twenty-two white doctors and nurses in which they were asked to offer explanations for racial inequality in health care. Results provide insight into how whiteness operates to provide white patients more often with appropriate health care and how colour-blind ideology can be adapted to accommodate naming white advantage and potential racial discrimination. However, even when naming mechanisms of white advantage in accessing resources, the white respondents avoided acknowledging how they are implicated in racial inequality in health care. We discuss the implications for understanding whiteness and colour-blind ideology.     

Task Type Affects Location of Language-Positive Cortical Regions by Repetitive Navigated Transcranial Magnetic Stimulation Mapping

Objectives

Recent repetitive TMS (rTMS) mapping protocols for language mapping revealed deficits of this method, mainly in posterior brain regions. Therefore this study analyzed the impact of different language tasks on the localization of language-positive brain regions and compared their effectiveness, especially with regard to posterior brain regions.

Methods

Nineteen healthy, right-handed subjects performed object naming, pseudoword reading, verb generation, and action naming during rTMS language mapping of the left hemisphere. Synchronically, 5 Hz/10 pulses were applied with a 0 ms delay

Results

The object naming task evoked the highest error rate (14%), followed by verb generation (13%) and action naming (11%). The latter revealed more errors in posterior than in anterior areas. Pseudoword reading barely generated errors, except for phonological paraphasias.

Conclusions

In general, among the evaluated language tasks, object naming is the most discriminative task to detect language-positive regions via rTMS. However, other tasks might be used for more specific questions.     

不同频率重复经颅磁刺激治疗脑卒中后失语症的效果观察

目的:探讨不同频率重复经颅磁刺激(Repeated transcranial magnetic stimulation,r TMS)治疗脑卒中后失语症的临床效果。方法:选取2015年10月至2018年10月我院收治的脑卒中后失语症患者80例,采用随机数字表法将患者分为两组,低频组患者给予低频r TMS治疗,高频组患者给予高频r TMS治疗。比较两组患者治疗后的西方失语成套测验(Western Aphasia Battery,WAB)各项评分,治疗前后日常生活交流能力检查(Communicative abilities in daily living test,CADL)评分、视图命名得分及命名反应时间的变化。结果:治疗后,两组患者的自发语言、听理解、命名、复述和失语商(Aphasia quotient,AQ)评分比较均无统计学差异(P0.05);两组CADL评分和视图命名得分均较治疗前显著升高(P0.05),但两组间比较无统计学差异(P0.05);两组命名反应时间均较治疗前显著缩短,且高频组显著短于低频组(P0.05)。结论:高频r TMS与低频r TMS均可显著改善脑卒中后失语症患者的自发语言、听理解、命名、复述及日常生活交流能力,但高频r TMS在缩短命名反应时间方面具有更好的效果。