A peroxiredoxin cDNA from Taiwanofungus camphorata: role of Cys31 in dimerization

Peroxiredoxins (Prxs) play important roles in antioxidant defense and redox signaling pathways. A Prx isozyme cDNA (TcPrx2, 745 bp, EF552425) was cloned from Taiwanofungus camphorata and its recombinant protein was overexpressed. The purified protein was shown to exist predominantly as a dimer by sodium dodecyl sulfate-polyacrylamide gel electrolysis in the absence of a reducing agent. The protein in its dimeric form showed no detectable Prx activity. However, the protein showed increased Prx activity with increasing dithiothreitol concentration which correlates with dissociation of the dimer into monomer. The TcPrx2 contains two Cys residues. The Cys(60) located in the conserved active site is the putative active peroxidatic Cys. The role of Cys(31) was investigated by site-directed mutagenesis. The C31S mutant (C(31) → S(31)) exists predominantly as a monomer with noticeable Prx activity. The Prx activity of the mutant was higher than that of the corresponding wild-type protein by nearly twofold at 12 μg/mL. The substrate preference of the mutant was H2O2 > cumene peroxide > t-butyl peroxide. The Michaelis constant (K M) value for H2O2 of the mutant was 0.11 mM. The mutant enzyme was active under a broad pH range from 6 to 10. The results suggest a role of Cys(31) in dimerization of the TcPrx2, a role which, at least in part, may be involved in determining the activity of Prx. The C(31) residue does not function as a resolving Cys and therefore the TcPrx2 must follow the reaction mechanism of 1-Cys Prx. This TcPrx2 represents a new isoform of Prx family

Various criteria in the evaluation of biomedical named entity recognition

BACKGROUND: Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most frequently used for training and testing biomedical named entity recognition (Bio-NER) systems. JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance. This paper details these differences and describes alternative criteria. We then examine the impact of different criteria and annotation schemes on system performance by retesting systems participated in the above two tasks. RESULTS: To analyze the difference between JNLPBA's and BioCreAtIvE's evaluation, we conduct Experiment 1 to evaluate the top four JNLPBA systems using BioCreAtIvE's classification scheme. We then compare them with the top four BioCreAtIvE systems. Among them, three systems participated in both tasks, and each has an F-score lower on JNLPBA than on BioCreAtIvE. In Experiment 2, we apply hypothesis testing and correlation coefficient to find alternatives to BioCreAtIvE's evaluation scheme. It shows that right-match and left-match criteria have no significant difference with BioCreAtIvE. In Experiment 3, we propose a customized relaxed-match criterion that uses right match and merges JNLPBA's five NE classes into two, which achieves an F-score of 81.5%. In Experiment 4, we evaluate a range of five matching criteria from loose to strict on the top JNLPBA system and examine the percentage of false negatives. Our experiment gives the relative change in precision, recall and F-score as matching criteria are relaxed. CONCLUSION: In many applications, biomedical NEs could have several acceptable tags, which might just differ in their left or right boundaries. However, most corpora annotate only one of them. In our experiment, we found that right match and left match can be appropriate alternatives to JNLPBA and BioCreAtIvE's matching criteria. In addition, our relaxed-match criterion demonstrates that users can define their own relaxed criteria that correspond more realistically to their application requirements

Morphological and phylogenetic characterisation of novel Cytospora species associated with mangroves

Mangroves are relatively unexplored habitats and have been shown to harbour a number of novel species of fungi. In this study, samples of microfungi were collected from symptomatic branches, stem and leaves of the mangrove species Xylocarpus granatum, X. moluccensis and Lumnitzera racemosa and examined morphologically. The phylogeny recovered supports our morphological data to introduce three new species, Cytospora lumnitzericola, C. thailandica and C. xylocarpi. In addition, a combined multi-gene DNA sequence dataset (ITS, LSU, ACT and RPB2) was analysed to investigate phylogenetic relationships of isolates and help in a more reliable species identification

Asteroid Spin-Rate Study using the Intermediate Palomar Transient Factory

Two dedicated asteroid rotation-period surveys have been carried out using data taken on January 6-9 and February 20-23 of 2014 by the Intermediate Palomar Transient Factory (iPTF) in the $R$~band with $\sim 20$-min cadence. The total survey area covered 174~deg$^2$ in the ecliptic plane. Reliable rotation periods for 1,438 asteroids are obtained from a larger data set of 6,551 mostly main-belt asteroids, each with $\geq 10$~detections. Analysis of 1751, PTF based, reliable rotation periods clearly shows the "spin barrier" at $\sim 2$~hours for "rubble-pile" asteroids. We also found a new large-sized super-fast rotator, 2005 UW163 (Chang et al., 2014), and other five candidates as well. Our spin-rate distributions of asteroids with $3 < D < 15$~km shows number decrease when frequency greater than 5 rev/day, which is consistent to that of the Asteroid Light Curve Database (LCDB, Warner et al., 2009) and the result of (Masiero et al., 2009). We found the discrepancy in the spin-rate distribution between our result and (Pravec et al., 2008, update 2014-04-20) is mainly from asteroids with $\Delta m < 0.2$ mag that might be primarily due to different survey strategies. For asteroids with $D \leq 3$~km, we found a significant number drop at $f = 6$ rev/day. The YORP effect timescale for small-sized asteroid is shorter that makes more elongate objets spun up to reach their spin-rate limit and results in break-up. The K-S test suggests a possible difference in the spin-rate distributions of C- and S-type asteroids. We also find that C-type asteroids have a smaller spin-rate limit than the S-type, which agrees with the general sense that the C-type has lower bulk density than the S-type.Comment: Submitted to ApJ (Jan, 2015). Accepted by ApJ (June, 2015). The whole set of the folded lightcurves will be available on the published articl