The Gene Ontology in 2010: extensions and refinements

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use

Cross-Product Extensions of the Gene Ontology

The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries

A MOD(ern) perspective on literature curation

Curation of biological data is a multi-faceted task whose goal is to create a structured, comprehensive, integrated, and accurate resource of current biological knowledge. These structured data facilitate the work of the scientific community by providing knowledge about genes or genomes and by generating validated connections between the data that yield new information and stimulate new research approaches. For the model organism databases (MODs), an important source of data is research publications. Every published paper containing experimental information about a particular model organism is a candidate for curation. All such papers are examined carefully by curators for relevant information. Here, four curators from different MODs describe the literature curation process and highlight approaches taken by the four MODs to address: (1) the decision process by which papers are selected, and (2) the identification and prioritization of the data contained in the paper. We will highlight some of the challenges that MOD biocurators face, and point to ways in which researchers and publishers can support the work of biocurators and the value of such support

Freezing of sputum as a way to improve the applicability of sputum studies

Rationale: Sputum examination is a valuable research tool to study airway diseases, but the requirement to process the samples within 2 hours of their collection poses limitations to its wider applicability. A way to bypass this hurdle would be to freeze the sample at the time of collection and to examine it at a later stage.Methods and Subjects: We developed a protocol for freezing of sputum upon collection by adding dimethylsulfoxide to it. We tested the reproducibility of cell counts in frozen samples and in fresh portions from the same sputum specimens. We took sputum from 41 asthmatics (18 males) with different levels of control of their disease: 19 of the samples were spontaneously produced and 22 were induced with hypertonic saline.Results: Significant correlations (p<0.05) were established between the total cell counts, the relative and absolute number of neutrophils, eosinophils and macrophages in the paired fresh and frozen sputum samples. Cell viability in frozen sputum was slightly but consistently lower. Only one frozen sample had viability < 50%. Outcomes in paired samples from induced sputum had better reproducibility than the spontaneous ones.Conclusion: Examination of frozen sputum samples does not change total cell counts and differential cell counts, despite consistently affecting cell viability compared with fresh sputum cellularity. Still cell viability in frozen sputum was above 50% in all but one examined specimens

Methods of classification for women undergoing induction of labour: a systematic review and novel classification system

Background: The lack of reproducible methods for classifying women having an induction of labour (IOL) has led to controversies regarding the association of IOL and health outcomes for mother and baby. Objectives: To identify research papers that describe a methodology for classifying women having an IOL, and to evaluate the utility of these methods of classification for clinical, research and surveillance purposes. Search strategy: We conducted electronic searches in CINAHL, EMBASE and WEB of KNOWLEDGE from database inception until Oct 2013 and searched reference lists. Selection criteria: Two reviewers independently assessed eligibility. Studies had to describe a method for classifying women with an IOL using a minimum of two categories, regardless of whether or not this was the main purpose of the study. Data collection: Data were extracted on study characteristics, quality and results. Pre-specified criteria were used to evaluate the utility of these methods of classification for IOL. Main results: Seven studies met the inclusion criteria. All studies categorised women according to the presence or absence of a medical indication for IOL. Uncertainties and/or deficiencies were identified across all methods of classification related to the criteria of total inclusivity, reproducibility, clinical utility, implementability and data availability limiting their usefulness. Conclusion: Current methods of classifying women with an IOL are inadequate for clinical, research and surveillance purposes. Limitations with classification systems based on medical indications suggest that an alternative method of classification is required for women having IOL

Sodium-calcium exchanger and multiple sodium channel isoforms in intra-epidermal nerve terminals

<p>Abstract</p> <p>Background</p> <p>Nociception requires transduction and impulse electrogenesis in nerve fibers which innervate the body surface, including the skin. However, the molecular substrates for transduction and action potential initiation in nociceptors are incompletely understood. In this study, we examined the expression and distribution of Na⁺/Ca²⁺exchanger (NCX) and voltage-gated sodium channel isoforms in intra-epidermal free nerve terminals.</p> <p>Results</p> <p>Small diameter DRG neurons exhibited robust NCX2, but not NCX1 or NCX3 immunolabeling, and virtually all PGP 9.5-positive intra-epidermal free nerve terminals displayed NCX2 immunoreactivity. Sodium channel Na_V1.1 was not detectable in free nerve endings. In contrast, the majority of nerve terminals displayed detectable levels of expression of Na_V1.6, Na_V1.7, Na_V1.8 and Na_V1.9. Sodium channel immunoreactivity in the free nerve endings extended from the dermal boundary to the terminal tip. A similar pattern of NCX and sodium channel immunolabeling was observed in DRG neurons <it>in vitro</it>.</p> <p>Conclusions</p> <p>NCX2, as well as Na_V1.6, Na_V1.7, Na_V1.8 and Na_V1.9, are present in most intra-epidermal free nerve endings. The presence of NCX2, together with multiple sodium channel isoforms, in free nerve endings may have important functional implications.</p

Mutations at opposite ends of the DIII/S4-S5 linker of sodium channel NaV1.7 produce distinct pain disorders

<p>Abstract</p> <p>Background</p> <p>Two groups of gain-of-function mutations in sodium channel Na_V1.7, which are expressed in dorsal root ganglion (DRG) neurons, produce two clinically-distinct pain syndromes - inherited erythromelalgia (IEM) and paroxysmal extreme pain disorder (PEPD). IEM is characterized by intermittent burning pain and skin redness in the feet or hands, triggered by warmth or mild exercise, while PEPD is characterized by episodes of rectal, ocular and mandibular pain accompanied with skin flushing, triggered by bowel movement and perianal stimulation. Most of the IEM mutations are located within channel domains I and II, while most of the PEPD mutations are located within domains III and IV. The structural dichotomy parallels the biophysical effects of the two types of mutations, with IEM mutations shifting voltage-dependence of Na_V1.7 activation in a hyperpolarized direction, and PEPD mutations shifting fast-inactivation of Na_V1.7 in a depolarized direction. While four IEM and four PEPD mutations are located within cytoplasmic linkers joining segments 4 and 5 (S4-S5 linkers) in the different domains (IEM: domains I and II; PEPD: domains III and IV), no S4-S5 linker has been reported to house both IEM and PEPD mutations thus far.</p> <p>Results</p> <p>We have identified a new IEM mutation P1308L within the C-terminus of the DIII/S4-S5 linker of Na_V1.7, ten amino acids from a known PEPD mutation V1298F which is located within the N-terminus of this linker. We used voltage-clamp to compare the biophysical properties of the two mutant channels and current-clamp to study their effects on DRG neuron excitability. We confirm that P1308L and V1298F behave as prototypical IEM and PEPD mutations, respectively. We also show that DRG neurons expressing either P1308L or V1298F become hyperexcitable, compared to DRG neurons expressing wild-type channels.</p> <p>Conclusions</p> <p>Our results provide evidence for differential roles of the DIII/S4-S5 linker N- and C-termini in channel inactivation and activation, and demonstrate the cellular basis for pain in patients carrying these mutations.</p

Single-step purification of full-length human androgen receptor

The full-length human androgen receptor with an N-terminal biotin acceptor peptide tag was overexpressed in Spodoptera frugiperda cells in the presence of 1 µM dihydrotestosterone. Site-specific biotinylation of BAP was achieved in vivo by co-expression of E. coli biotin holoenzyme synthetase. The androgen receptor was purified by single-step affinity chromatography using Streptavidin Mutein Matrix under native conditions. The resultant protein was active, stable, 95% homogeneous, and we obtained sufficient yield for use in functional and structural studies

PatMatch: a program for finding patterns in peptide and nucleotide sequences

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible pattern syntax based on regular expressions. A recent upgrade has improved performance and now supports both mismatches and wildcards in a single pattern. This enhancement has been achieved by replacing the previous searching algorithm, scan_for_matches [D'Souza et al. (1997), Trends in Genetics, 13, 497–498], with nondeterministic-reverse grep (NR-grep), a general pattern matching tool that allows for approximate string matching [Navarro (2001), Software Practice and Experience, 31, 1265–1312]. We have tailored NR-grep to be used for DNA and protein searches with PatMatch. The stand-alone version of the software can be adapted for use with any sequence dataset and is available for download at The Arabidopsis Information Resource (TAIR) at . The PatMatch server is available on the web at for searching Arabidopsis thaliana sequences