Genome-wide identification and functional analysis of JmjC domain-containing genes in flower development of Rosa chinensis

Plant Molecular Biology - We genome-wide identified 28 JmjC domain-containing genes, further spatio-temporal expression profiling and genetic analysis defined them as epigenetic regulators in...     

A semi-supervised support vector machine approach for parameter setting in motor imagery-based brain computer interfaces

Parameter setting plays an important role for improving the performance of a brain computer interface (BCI). Currently, parameters (e.g. channels and frequency band) are often manually selected. It is time-consuming and not easy to obtain an optimal combination of parameters for a BCI. In this paper, motor imagery-based BCIs are considered, in which channels and frequency band are key parameters. First, a semi-supervised support vector machine algorithm is proposed for automatically selecting a set of channels with given frequency band. Next, this algorithm is extended for joint channel-frequency selection. In this approach, both training data with labels and test data without labels are used for training a classifier. Hence it can be used in small training data case. Finally, our algorithms are applied to a BCI competition data set. Our data analysis results show that these algorithms are effective for selection of frequency band and channels when the training data set is small.     

Cloning,expression, and identification of anti‐carbofuran single chain Fv gene

Phage display method was used to clone anti‐carbofuran (CBF) single chain Fv (scFv) gene. The heavy chain and light chain variable region genes were amplified by the polymerase chain reaction from the CBF‐specific hybridoma cell lines 5D3 and assembled as a scFv DNA fragment with linker peptide (Gly₄Ser)₃. The scFv DNA fragment was cloned into M13 phagemid vector pCANTAB5E and the anti‐CBF antibody libraries were then constructed. After one round of panning with CBF‐ovalbumin (CBF‐OVA) as a conjugate, antigen‐binding positive recombinant phage clones were successfully selected by enzyme‐linked immunosorbent assay (ELISA). The positive phages were used to infect Escherichia coli HB2151 cells and the expression of the soluble scFv antibodies was then induced by IPTG. The scFv antibody was about 31 kDa by SDS‐PAGE and showed HRP‐anti‐E‐tag antibody‐recognized activity by Western blotting. The indirect competitive ELISA (icELISA) showed that the recombinant scFv antibody could competitively combine with CBF, with the IC₅₀ value of 1.07 ng/mL. The cross reactivity studies showed that the anti‐CBF scFv antibody, similar to the parent monoclonal antibody, poses high specificity to CBF and has little reactivity to the analogs. Taken together, these findings suggest that the recombinant scFv antibody can be used for further developing immunoassay method for CBF. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Reproducibility and discriminability of brain patterns of semantic categories enhanced by congruent audiovisual stimuli

One of the central questions in cognitive neuroscience is the precise neural representation, or brain pattern, associated with a semantic category. In this study, we explored the influence of audiovisual stimuli on the brain patterns of concepts or semantic categories through a functional magnetic resonance imaging (fMRI) experiment. We used a pattern search method to extract brain patterns corresponding to two semantic categories: "old people" and "young people." These brain patterns were elicited by semantically congruent audiovisual, semantically incongruent audiovisual, unimodal visual, and unimodal auditory stimuli belonging to the two semantic categories. We calculated the reproducibility index, which measures the similarity of the patterns within the same category. We also decoded the semantic categories from these brain patterns. The decoding accuracy reflects the discriminability of the brain patterns between two categories. The results showed that both the reproducibility index of brain patterns and the decoding accuracy were significantly higher for semantically congruent audiovisual stimuli than for unimodal visual and unimodal auditory stimuli, while the semantically incongruent stimuli did not elicit brain patterns with significantly higher reproducibility index or decoding accuracy. Thus, the semantically congruent audiovisual stimuli enhanced the within-class reproducibility of brain patterns and the between-class discriminability of brain patterns, and facilitate neural representations of semantic categories or concepts. Furthermore, we analyzed the brain activity in superior temporal sulcus and middle temporal gyrus (STS/MTG). The strength of the fMRI signal and the reproducibility index were enhanced by the semantically congruent audiovisual stimuli. Our results support the use of the reproducibility index as a potential tool to supplement the fMRI signal amplitude for evaluating multimodal integration.     

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-Reward-Related Genes among Mammals

Background

The giant panda has an interesting bamboo diet unlike the other species in the order of Carnivora. The umami taste receptor gene T1R1 has been identified as a pseudogene during its genome sequencing project and confirmed using a different giant panda sample. The estimated mutation time for this gene is about 4.2 Myr. Such mutation coincided with the giant panda''s dietary change and also reinforced its herbivorous life style. However, as this gene is preserved in herbivores such as cow and horse, we need to look for other reasons behind the giant panda''s diet switch.

Methodology/Principal Findings

Since taste is part of the reward properties of food related to its energy and nutrition contents, we did a systematic analysis on those genes involved in the appetite-reward system for the giant panda. We extracted the giant panda sequence information for those genes and compared with the human sequence first and then with seven other species including chimpanzee, mouse, rat, dog, cat, horse, and cow. Orthologs in panda were further analyzed based on the coding region, Kozak consensus sequence, and potential microRNA binding of those genes.

Conclusions/Significance

Our results revealed an interesting dopamine metabolic involvement in the panda''s food choice. This finding suggests a new direction for molecular evolution studies behind the panda''s dietary switch.     

Expression of a metagenome-derived fumarate reductase from marine microorganisms and its characterization

A potential novel fumarate reductase gene designated frd1A was isolated by screening a marine metagenomic library through a sequence-based strategy. Sequence analyses indicated that Frd1A and other putative fumarate reductases were closely related. The putative fumarate reductase gene was subcloned into a pETBlue-2 vector and expressed in Escherichia coli Tuner(DE3)pLac? cells. The recombinant protein was purified to homogeneity. Functional characterization by high-performance liquid chromatography demonstrated that the recombinant Frd1A protein could catalyze the hydrogenation of fumarate to succinate acid. The Frd1A protein displayed an optimal activity at pH 7.0 and 28 °C, which could be stimulated by adding metal ions such as Zn²⁺ and Mg²⁺. The Frd1A enzyme showed a comparable affinity and catalytic efficiency under optimal reaction conditions: k _m?=0.227 mmol/L, v _max= 29.9 U/mg, and k _cat/k _m=5.44?×?10⁴ per mol/s. The identification of Frd1A protein underscores the potential of marine metagenome screening for novel biomolecules.     

GSTP1 Ile105Val polymorphism and colorectal cancer risk: An updated analysis

Background

Many studies have investigated the association between the Glutathione S transferase-P1 (GSTP1) Ile105Val polymorphism and colorectal cancer (CRC) susceptibility, but the results were conflicting. The aim of this study is to quantitatively summarize the relationship between this polymorphism and CRC risk.

Methods

Two investigators independently searched the Medline, Embase, China National Knowledge Infrastructure (CNKI) and Chinese Biomedicine databases for studies published before December 2012. Summary odds ratios (ORs) and 95% confidence intervals (95% CIs) for GSTP1 polymorphism and CRC were calculated in a fixed-effects model (the Mantel–Haenszel method) and a random-effects model (the DerSimonian and Laird method) when appropriate.

Results

This meta-analysis included 29 case–control studies, which included 8160 CRC cases and 10,450 controls. Overall, the variant genotypes (ValVal and IleVal) of the Ile105Val were not associated with CRC risk when compared with the wild-type IleIle homozygote. Similarly, no associations were found in the dominant and recessive models. When stratifying for ethnicity, source of controls, study sample size and genotyping methods, no evidence of significant association was observed in any subgroup, except among those studies taking others as genotyping methods (recessive model, OR = 0.71, 95%CI = 0.52–0.96). Limiting the analysis to the studies within Hardy–Weinberg equilibrium, the results were persistent and robust. No publication bias was found in the present study.

Conclusion

This updated meta-analysis suggests that the GSTP1 Ile105Val polymorphism may not be associated with CRC risk, while the observed decrease in risk of CRC may be due to small-study bias.     

Synthesis and cytotoxic activity of 17-carboxylic acid modified 23-hydroxy betulinic acid ester derivatives

New 17-carboxylic acid modified 23-hydroxy betulinic acid ester derivatives were prepared and tested for cytotoxic activity on five cancer cell lines in vitro: all tested compounds showed stronger cytotoxic activity than 23-hydroxy betulinic acid and betulinic acid. In addition, compound 5a was tested for anti-tumor activity in vivo: it had much better anti-tumor activity than 23-OH betulinic acid and had similar anti-tumor activity with cyclophosphamide and 5-fluorouracil.     

The B‐box protein BBX19 suppresses seed germination via induction of ABI5

Seed germination is a fundamental process in the plant life cycle and is regulated by functionally opposing internal and external inputs. Here we explored the role of a negative regulator of photomorphogenesis, a B‐box‐containing protein (BBX19), as a molecular link between the inhibitory action of the phytohormone abscisic acid (ABA) and the promoting role of light in germination. We show that seeds of BBX19‐overexpressing lines, in contrast to those of BBX19 RNA interference lines, display ABA hypersensitivity, albeit independently of elongated hypocotyl 5 (HY5). Moreover, we establish that BBX19 functions neither via perturbation of GA signaling, the ABA antagonistic phytohormone, nor through interference with the DELLA protein germination repressors. Rather, BBX19 functions as an inducer of ABA INSENSITIVE5 (ABI5) by binding to the light‐responsive GT1 motifs in the gene promoter. In summary, we identify BBX19 as a regulatory checkpoint, directing diverse developmental processes and tailoring adaptive responses to distinct endogenous and exogenous signals.