Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation

Background: Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. Results: We employ the Textpresso category-based information retrieval and extraction system http://www.textpresso.org webcite, developed by WormBase to explore how Textpresso might improve the efficiency with which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology. Using a training set of sentences that describe results of localization experiments in the published literature, we generated three new curation task-specific categories (Cellular Components, Assay Terms, and Verbs) containing words and phrases associated with reports of experimentally determined subcellular localization. We compared the results of manual curation to that of Textpresso queries that searched the full text of articles for sentences containing terms from each of the three new categories plus the name of a previously uncurated C. elegans protein, and found that Textpresso searches identified curatable papers with recall and precision rates of 79.1% and 61.8%, respectively (F-score of 69.5%), when compared to manual curation. Within those documents, Textpresso identified relevant sentences with recall and precision rates of 30.3% and 80.1% (F-score of 44.0%). From returned sentences, curators were able to make 66.2% of all possible experimentally supported GO Cellular Component annotations with 97.3% precision (F-score of 78.8%). Measuring the relative efficiencies of Textpresso-based versus manual curation we find that Textpresso has the potential to increase curation efficiency by at least 8-fold, and perhaps as much as 15-fold, given differences in individual curatorial speed. Conclusion: Textpresso is an effective tool for improving the efficiency of manual, experimentally based curation. Incorporating a Textpresso-based Cellular Component curation pipeline at WormBase has allowed us to transition from strictly manual curation of this data type to a more efficient pipeline of computer-assisted validation. Continued development of curation task-specific Textpresso categories will provide an invaluable resource for genomics databases that rely heavily on manual curation

Synovitis and bone inflammation in early rheumatoid arthritis: high-resolution multi-pinhole SPECT versus MRI

PURPOSEWe aimed to assess the relationship between bone inflammation in multi-pinhole single-photon emission computed tomography (MPH-SPECT) and synovitis detected by magnetic resonance imaging (MRI) in early rheumatoid arthritis patients. MATERIALS AND METHODSMPH-SPECT with technetium dicarboxypropanedisphosphonate (Tc-99mDPD) and 3 Tesla MRI were performed in 10 early rheumatoid arthritis patients. Eighty finger joint sites were assessed for increased osteoblastic activity using visual and region-of-interest (ROI) analysis. Presence of joint inflammation in MRI was investigated using the subscores of the rheumatoid arthritis MRI score. RESULTSTc-99mDPD uptake was increased in 38 (47.5%) and 22 (27.5%) joint sites as determined by visual and ROI analysis, respectively. A total of 32 (84.2%) sites with increased bone metabolism showed a normal MRI bone signal. The MPHSPECT uptake ratio was elevated only in the subgroup with severe synovitis (P < 0.001). CONCLUSIONIn early rheumatoid arthritis, molecular imaging with MPHSPECT detects higher rates of inflammatory bone involvement compared to MRI. Our preliminary data suggest that osteitis is related to severe synovitis

Time Dependence of Fluoride Uptake in Hydroxyapatite

Fluoridation of enamel is believed to provide an effective tool to protect teeth from caries, but there is still little information on the time scale of fluoride uptake. In this study, highly compressed pellets of hydroxyapatite are used as first-order model systems to approximate the mineral component of natural enamel for investigations on the time-dependence of fluoride uptake. We found that both the overall amount of fluoride as well as the mean thickness of the fluoridated surface layer cannot be extended to any values just by increasing the application time of a fluoride containing agent. Instead, both parameters start to become constant on a time scale of about 3 min. The present results as obtained on a synthetic model “tooth” show that the time scale to provide the maximum amount of fluoride possible is of the same order of magnitude as that in usual daily practice in dental care when applying toothpastes or mouth rinses

Biotransformation of Various Substituted Aromatic Compounds to Chiral Dihydrodihydroxy Derivatives

The biotransformation of four different classes of aromatic compounds by the Escherichia coli strain DH5α(pTCB 144), which contained the chlorobenzene dioxygenase (CDO) from Pseudomonas sp. strain P51, was examined. CDO oxidized biphenyl as well as monochlorobiphenyls to the corresponding cis-2,3-dihydro-2,3-dihydroxy derivatives, whereby oxidation occurred on the unsubstituted ring. No higher substituted biphenyls were oxidized. The absolute configurations of several monosubstituted cis-benzene dihydrodiols formed by CDO were determined. All had an S configuration at the carbon atom in meta position to the substituent on the benzene nucleus. With one exception, the enantiomeric excess of several 1,4-disubstituted cis-benzene dihydrodiols formed by CDO was higher than that of the products formed by two toluene dioxygenases. Naphthalene was oxidized to enantiomerically pure (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. All absolute configurations were identical to those of the products formed by toluene dioxygenases of Pseudomonas putida UV4 and P. putida F39/D. The formation rate of (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene was significantly higher (about 45 to 200%) than those of several monosubstituted cis-benzene dihydrodiols and more than four times higher than the formation rate of cis-benzene dihydrodiol. A new gas chromatographic method was developed to determine the enantiomeric excess of the oxidation products

<i>Corynebacterium glutamicum</i> Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology

Targeted top-down strategies for genome reduction are considered to have a high potential for providing robust basic strains for synthetic biology and industrial biotechnology. Recently, we created a library of 26 genome-reduced strains of <i>Corynebacterium glutamicum</i> carrying broad deletions in single gene clusters and showing wild-type-like biological fitness. Here, we proceeded with combinatorial deletions of these irrelevant gene clusters in two parallel orders, and the resulting library of 28 strains was characterized under various environmental conditions. The final chassis strain C1* carries a genome reduction of 13.4% (412 deleted genes) and shows wild-type-like growth behavior in defined medium with d-glucose as carbon and energy source. Moreover, C1* proves to be robust against several stresses (including oxygen limitation) and shows long-term growth stability under defined and complex medium conditions. In addition to providing a novel prokaryotic chassis strain, our results comprise a large strain library and a revised genome annotation list, which will be valuable sources for future systemic studies of <i>C. glutamicum</i>