Learning string similarity measures for gene/protein name dictionary look-up using logistic regression

MOTIVATION: One of the bottlenecks of biomedical data integration is variation of terms. Exact string matching often fails to associate a name with its biological concept, i.e. ID or accession number in the database, due to seemingly small differences of names. Soft string matching potentially enables us to find the relevant ID by considering the similarity between the names. However, the accuracy of soft matching highly depends on the similarity measure employed. RESULTS: We used logistic regression for learning a string similarity measure from a dictionary. Experiments using several large-scale gene/protein name dictionaries showed that the logistic regression-based similarity measure outperforms existing similarity measures in dictionary look-up tasks. AVAILABILITY: A dictionary look-up system using the similarity measures described in this article is available at http://text0.mib.man.ac.uk/software/mldic/.     

Effects of inbreeding on variation in diapause duration and early fecundity in the Kanzawa spider mite

In arthropods, both diapause duration and ability to produce eggs in early adult life (early fecundity) are important life‐history traits for successful settling in a new habitat. In herbivorous spider mites (Acari: Tetranychidae), inbreeding frequently occurs because new colonies are established by only one or a few females. In the present study, we investigated the impact of inbreeding on the phenotypic variance in diapause duration and early fecundity in the Kanzawa spider mite, Tetranychus kanzawai Kishida. Diapause duration was compared between the inbreeding treatment (strongly inbred strains) and the control (strains immediately taken from the stock culture) under winter‐mimicking laboratory conditions. The variance in diapause duration was smaller in the inbreeding treatment than in the control, though the magnitude of decrease of variance was less than expected. On the other hand, early fecundity did not show any reduction of variance. The present results revealed that inbreeding reduces phenotypic variation, as expected in theory.     

Mechanisms of the selenium tolerance of the Arabidopsis thaliana knockout mutant of sulfate transporter SULTR1;2

We investigated the mechanism of selenium (Se) tolerance using an Arabidopsis thaliana knockout mutant of a sulfate transporter, sultr1;2. Se stress inhibited plant growth, decreased chlorophyll contents, and increased protein oxidation and lipid peroxidation in the wild type, whereas the sultr1;2 mutation mitigated damage of these forms, indicating that sultr1;2 is more tolerant of Se than the wild type is. The accumulation of symplastic Se was suppressed in sultr1;2 as compared to the wild type, and the chemical speciation of Se in the mutant was different from that in the wild type. Regardless of Se stress, the activities of ascorbate peroxidase, catalase, and peroxidase in the mutant were higher than in the wild type, while the activity of superoxide dismutase in the mutant was the same as in the wild type. These results suggest that the sultr1;2 mutation confers Se tolerance on Arabidopsis by decreasing symplastic Se and maintaining antioxidant enzyme activities.     

Inhibitory effects of methylglyoxal on light-induced stomatal opening and inward K+ channel activity in Arabidopsis

Methylglyoxal (MG) is a reactive aldehyde derived by glycolysis. In Arabidopsis, MG inhibited light-induced stomatal opening in a dose-dependent manner. It significantly inhibited both inward-rectifying potassium (K(in)) channels in guard-cell protoplasts and an Arabidopsis K(in) channel, KAT1, heterologously expressed in Xenopus oocytes. Thus it appears that MG inhibition of stomatal opening involves MG inhibition of K(+) influx into guard cells.     

Effect of γ irradiation on the fatty acid composition of soybean and soybean oil

Food irradiation is a form of food processing to extend the shelf life and reduce spoilage of food. We examined the effects of γ radiation on the fatty acid composition, lipid peroxidation level, and antioxidative activity of soybean and soybean oil which both contain a large amount of unsaturated fatty acids. Irradiation at 10 to 80 kGy under aerobic conditions did not markedly change the fatty acid composition of soybean. While 10-kGy irradiation did not markedly affect the fatty acid composition of soybean oil under either aerobic or anaerobic conditions, 40-kGy irradiation considerably altered the fatty acid composition of soybean oil under aerobic conditions, but not under anaerobic conditions. Moreover, 40-kGy irradiation produced a significant amount of trans fatty acids under aerobic conditions, but not under anaerobic conditions. Irradiating soybean oil induced lipid peroxidation and reduced the radical scavenging activity under aerobic conditions, but had no effect under anaerobic conditions. These results indicate that the fatty acid composition of soybean was not markedly affected by radiation at 10 kGy, and that anaerobic conditions reduced the degradation of soybean oil that occurred with high doses of γ radiation.     

Magenta pigment produced by fungus

A fungus producing magenta was isolated from cellulosic material by visual observation on Czapek's agar media and the product was conventionally analyzed. The fungal strain that produced magenta pigment was closely related to Phoma herbarum. The type of fibers added to Czapek's medium influenced which pigments were produced. Mycelia attached to the surface of nylon-6 and excreted magenta pigment into the fibers. The pigment structure was partially determined. This is the first report of the production of magenta pigment by a microorganism specifically in the presence of nylon-6 fibers, via an unknown mechanism. This phenomenon raises the question of why and how the fungus disperses the pigment inside the fiber and suggests that fabrics can be dyed using microorganisms.     

Crystal structure and some properties of a major house dust mite allergen, Derf 2

Pyroglyphid house dust mites are a major source of allergens in house dust. Mite allergens sensitize and induce asthma, rhinitis, and eczema in a large portion of patients with allergic diseases. Here, the crystal structure of a major mite allergen, Derf 2, derived from Dermatophagoides farinae was solved by single isomorphous replacement method with anomalous scattering (SIRAS) at 2.1A resolution. The present study also demonstrated that the conformation of the allergen was critical in the determination of Th1/Th2 shift based on physicochemical and immunological analyses. This indicates that rigidly folded and singly dispersed structure is essentially required for the generation of Th2 type cells by the allergen, while conformational variant protein leads to Th1 skewing, irrespective of the same amino acid sequence. This structure/function relationship may allow us to develop a novel strategy for hyposensitization therapy in patients with allergic diseases triggered by house dust mite allergens.     

Effect of benzylic oxygen on the cytotoxic activity for colon 26 cell line of phenolic lignans

The cytotoxic activity for colon 26 cell line of matairesinol, oxidized matairesinol, 9,9'-epoxylignan and oxidized 9,9'-epoxylignan were examined. (-)-Matairesinol (Mat 1) showed greatest cytotoxic activity (LC(50)=9 microg/ml) of the lactone-type lignans. 7,7'-Oxomatairesinol having same steric configuration as that of (-)-matairesinol showed greater activity (LC(50)=25 microg/ml) than hydroxy or mono-oxomatairesinol. The activities of 9,9'-epoxylignan and 7,7'-oxo-9,9'-epoxylignan having same steric configurations as (-)-matairesinol were weaker than that of corresponding matairesinols. Different activity levels were observed between enantiomers.     

Proline and glycinebetaine induce antioxidant defense gene expression and suppress cell death in cultured tobacco cells under salt stress

Salt stress causes oxidative damage and cell death in plants. Plants accumulate proline and glycinebetaine (betaine) to mitigate detrimental effects of salt stress. The aim of this study was to investigate the protective effects of proline and betaine on cell death in NaCl-unadapted tobacco (Nicotiana tabacum) Bright Yellow-2 suspension-cultured cells subjected to salt stress. Salt stress increased reactive oxygen species (ROS) accumulation, lipid peroxidation, nuclear deformation and degradation, chromatin condensation, apoptosis-like cell death and ATP contents. Neither proline nor betaine affected apoptosis-like cell death and G(1) phase population, and increased ATP contents in the 200mM NaCl-stressed cells. However, both of them effectively decreased ROS accumulation and lipid peroxidation, and suppressed nuclear deformation and chromatin condensation induced by severe salt stress. Evans Blue staining experiment showed that both proline and betaine significantly suppressed increment of membrane permeability induced by 200mM NaCl. Furthermore, among the ROS scavenging antioxidant defense genes studied here, mRNA levels of salicylic acid-binding (SAbind) catalase (CAT) and lignin-forming peroxidase (POX) were found to be increased by proline and betaine under salt stress. It is concluded that both proline and betaine provide a protection against NaCl-induced cell death via decreasing level of ROS accumulation and lipid peroxidation as well as improvement of membrane integrity.     

Craniofacial malformation in R-spondin2 knockout mice

In vertebrates, craniofacial formation is accomplished by synergistic interaction of many small elements which are generated independently from distinct germ layers. Because of its complexity, the imbalance of one signaling cascade such as Wnt/β-catenin pathway easily leads to craniofacial malformation, which is the most frequent birth defect in humans. To investigate the developmental role of a newly identified activator of Wnt/β-catenin signaling, Rspo2, we generated and characterized Rspo2^−/− mice. We found CLP with mild facial skeletal defects in Rspo2^−/− mice. Additionally, Rspo2^−/− mice also exhibited distal limb loss and lung hypoplasia, and died immediately after birth with respiratory failure. We showed the apparent reduction of Wnt/β-catenin signaling activity at the branchial arch and the apical ectodermal ridge in Rspo2^−/− mice. These findings indicate that Rspo2 regulates midfacial, limb, and lung morphogenesis during development through the Wnt/β-catenin signaling.