Divergence in Enzymatic Activities in the Soybean GST Supergene Family Provides New Insight into the Evolutionary Dynamics of Whole-Genome Duplicates

Whole-genome duplication (WGD), or polyploidy, is a major force in plant genome evolution. A duplicate of all genes is present in the genome immediately following a WGD event. However, the evolutionary mechanisms responsible for the loss of, or retention and subsequent functional divergence of polyploidy-derived duplicates remain largely unknown. In this study we reconstructed the evolutionary history of the glutathione S-transferase (GST) gene family from the soybean genome, and identified 72 GST duplicated gene pairs formed by a recent Glycine-specific WGD event occurring approximately 13 Ma. We found that 72% of duplicated GST gene pairs experienced gene losses or pseudogenization, whereas 28% of GST gene pairs have been retained in the soybean genome. The GST pseudogenes were under relaxed selective constraints, whereas functional GSTs were subject to strong purifying selection. Plant GST genes play important roles in stress tolerance and detoxification metabolism. By examining the gene expression responses to abiotic stresses and enzymatic properties of the ancestral and current proteins, we found that polyploidy-derived GST duplicates show the divergence in enzymatic activities. Through site-directed mutagenesis of ancestral proteins, this study revealed that nonsynonymous substitutions of key amino acid sites play an important role in the divergence of enzymatic functions of polyploidy-derived GST duplicates. These findings provide new insights into the evolutionary and functional dynamics of polyploidy-derived duplicate genes.

Determination of the potential of induced pluripotent stem cells to differentiate into mouse nucleus pulposus cells in vitro

We determined the potential for induced pluripotent stem (iPS) cells to differentiate into nucleus pulposus (NP)-like cells in mice. iPS cells were generated from tail-tip fibroblasts. We used a pellet culture model with the aim of determining the applicability of iPS cell-based therapy to intervertebral disc degeneration (IVD). The cell pellet was cultured in an NP cell basal medium comprising Dulbecco's modified Eagle's medium supplemented with transforming growth factor beta 1, dexamethasone, ascorbate-2-phosphate, and 1% ITS-Premix. The pellet was evaluated by quantitative reverse transcription polymerase chain reaction, immunohistochemical staining, and biochemical composition. The differentiation of iPS cells into NP cells was demonstrated by the protein and mRNA expression levels of proteoglycan, collagen II, aggrecan, and CD24. Furthermore, increased hydroxyproline content and dimethylmethylene blue staining demonstrated that the collagen II and glycosaminoglycan content in the NP cells increased with time. We have shown that cultured mouse iPS cells can be induced to differentiate into NP cells. Such proof-of-concept opens up the possibility of producing patient-specific NP cells in a relatively simple and straightforward manner with high efficiency. We are confident that such cells could be immediately useful for the study of IVD disease.

Differential microRNA expression in signet-ring cell carcinoma compared with tubular adenocarcinoma of human gastric cancer

Gastric cancer is a disease with a heterogeneous pathology; its pathological mechanisms remain unclear because there is a poor understanding of its etiology. In this study, we identified differentially expressed microRNAs (miRNAs) among various gastric cancer subtypes. miRNA microarray analysis and bioinformatic analysis were used to compare miRNA expression between the signet-ring cell carcinoma and tubular adenocarcinoma subtypes of gastric cancer. Thirteen dysregulated miRNAs were identified in signet-ring cell carcinoma compared with tubular adenocarcinoma: miR-30a, miR-26b, miR-381, let-7i, miR-29c, miR-543, miR-499-3p, miR-628-3p, miR-524-5p, miR-181b, miR-1914, miR-663b, and miR-676. This is the first time that miR-499-3p, miR-628-3p, miR-524-5p, and miR-1914 have been identified in gastric cancer tissues. Bioinformatic analysis using target prediction algorithms indicated that these miRNAs are directly involved in gastric cancer pathogenesis and have different pathological mechanisms in various subtypes of signet-ring cell carcinoma and tubular adenocarcinoma. The miRNA expression patterns in different gastric adenocarcinoma subtypes may help discriminate between signet-ring cell and tubular gland cancer or other gastric cancer subtypes that would otherwise be difficult to identify using routine histological and immunohistochemical analyses. These preliminary data should be verified in further prospective studies.

Identification of a major quantitative trait locus for ear size induced by space flight in sweet corn

The development of molecular markers has contributed to progress in identifying the gene(s) responsible for favorable variations in maize studies. In this study, quantitative trait locus (QTL) mapping was conducted using simple sequence repeat markers in an F2 sweet corn population from a cross between parental line 1132 and space flight-induced mutant line 751 to identify the loci contributing to an increase in some yield traits. A primary mutated genomic region was located on chromosome 9. In total, 26 QTL were detected for eight yield-related traits and assembled into three clusters on chromosome 9. The largest QTL cluster at bin 9.02/03, primarily contributing to >10% of the phenotypic variation in ear and cob diameters, was likely due to a major QTL. Desired alleles of these QTL were provided by the mutant line 751. The primary action of the major mutant allele was an additive effect. Another mutant locus, which was induced in bin 9.01, increased cob and ear diameters by dominant genetic action.

Comparative study of clinicopathological significance, BIRC7, and STC2 expression between squamous cell/adenosquamous carcinomas and adenocarcinoma of gallbladder

Gallbladder cancers (GBCs) are uncommon, but highly aggressive cancers. The majority of GBCs are adenocarcinomas (ACs), but rare subtypes of GBCs such as squamous cell carcinoma (SC) and adenosquamous carcinoma (ASC) are observed as well. The clinicopathological characteristics of SC/ASC have not been well documented. Expressions of BIRC7 and STC2 were observed in some tumors. However, BIRC7 and STC2 expressions and clinical significances in gallbladder cancer have not been reported.In this study, the protein expressions of BIRC7 and STC2 in 46 SCs/ASCs and 80 ACs were measured using immunohistochemistry. We demonstrated that positive BIRC7 and STC2 expressions were significantly associated with large tumor mass (>3cm), high TNM stage and lymph node metastasis in SC/ASC and AC (p<0.05). Positive expression of BIRC7 was significantly associated with invasion of around tissues and organs in both SC/ASC and AC. Additionally, negative BIRC7 and STC2 expressions were significantly associated with surgical curability in AC. Univariate Kaplan-Meier analysis showed that BIRC7 and STC2 expressions, differentiation, tumor size, TNM stages, invasion, lymph node metastasis, and surgical curability were significantly associated with post-operative survival in both SC/ASC and AC patients(p < 0.001). Multivariate Cox regression analysis showed that positive BIRC7 and STC2 expressions are independent poor-prognostic factors in both SC/ASC and AC patients. Our study suggested that positive BIRC7 and STC2 expressions are closely correlated with clinical, pathological, and biological behaviors as well as poor-prognosis of gallbladder cancer.

Molecular evolution and expression divergence of the Populus polygalacturonase supergene family shed light on the evolution of increasingly complex organs in plants

Plant polygalacturonases (PGs) are involved in cell separation processes during many stages of plant development. Investigation into the diversification of this large gene family in land plants could shed light on the evolution of structural development. We conducted whole-genome annotation, molecular evolution and gene expression analyses of PG genes in five species of land plant: Populus, Arabidopsis, rice, Selaginella and Physcomitrella. We identified 75, 44, 16 and 11 PG genes from Populus, rice, Selaginella and Physcomitrella genomes, respectively, which were divided into three classes. We inferred rapid expansion of class I PG genes in Populus, Arabidopsis and rice, while copy numbers of classes II and III PG genes were relatively conserved in all five species. Populus, Arabidopsis and rice class I PG genes were under more relaxed selection constraints than class II PG genes, while this selective pressure divergence was not observed in Selaginella and Physcomitrella PG families. In addition, class I PG genes underwent marked expression divergence in Populus, rice and Selaginella. Our results suggest that PG gene expansion occurred after the divergence of the lycophytes and euphyllophytes, and this expansion was likely paralleled by the evolution of increasingly complex organs in land plants.

First Report of Leaf Spot Caused by Alternaria longipes on Atractylodes macrocephala in China

Atractylodes macrocephala Koidz. is a perennial herb that has been used in Chinese herbal medicine for centuries. During the summer of 2011, leaf spots were observed on leaves of A. macrocephala in Panan County of Zhejiang Province, China. Approximately 40% of the plants surveyed showed severe symptoms of leaf spot. At the initial stage of the infection, small, light brown spots appeared on the leaves that gradually became semicircular, oval, or irregular-shaped with dark brown or black centers surrounded by brown or light brown margins. The lesions enlarged and coalesced to form large areas of necrosis on leaves until entire leaves died. Eight fungal isolates were obtained from diseased A. macrocephala leaves by a tissue isolation method (1). Isolates were cultured on potato dextrose agar (PDA) plates at 25°C in darkness. Colonies on PDA were initially white and became grayish brown over time. Conidiophores were light brown with one or a few regular septa, mostly unbranched. Conidia were obclavate, dark brown, with three to eight transverse and zero to two longitudinal or oblique septa, and on average measured 35.1 (20 to 53) × 9.8 (5.8 to 13.3) μm (n = 20). The internal transcribed spacer (ITS) region of rDNA was amplified using the primers ITS1F/ITS4 and sequenced (GenBank Accession No. JQ004404). The ITS sequence had 99% identity over 545 bp with Alternaria longipes (Ellis & Everh.) E. W. Mason (GenBank Accession No. AY278835), a fungal pathogen reported to cause leaf spot on Smilax china in China (3). To further identify the fungus, we chose the Alternaria allergen gene (Alt a 1 gene), which aids in identifying species of Alternaria (2). Amplification of the Alt a 1 gene was conducted using primers Alt-for/Alt-rev and sequenced (GenBank Accession No. JQ004405). Sequence comparisons showed there was 97% sequence identity with Alternaria longipes (GenBank Accession No. AY563304). Pathogenicity tests were performed on detached healthy A. macrocephala leaves. Nine leaves were inoculated by placing a PDA plug (0.5 cm²) of mycelia on upper surfaces of the leaves. Another nine leaves treated with sterile PDA plugs served as a control. Leaves were incubated in three petri dishes with a 12-h photoperiod at 25°C and 95% relative humidity. After 7 days, the symptoms described above were observed on all inoculated leaves, whereas no symptoms developed on control leaves. Reisolation of the fungus from symptomatic leaf tissues on PDA confirmed that the causal agent was Alternaria longipes. This pathogenicity test was performed three times. The genus Alternaria is ubiquitous and includes both plant pathogenic and saprophytic species that may cause leaf spot and blight on numerous plants (3,4), but to our knowledge, our research demonstrated this is the first report of leaf spot on A. macrocephalae caused by Alternaria longipes in China. References: (1) O. D. Dhingra and J. B. Sinclair. Basic Plant Pathology Methods. CRC Press, Boca Raton, FL, 1995. (2) S. G. Hong et al. Fungal Genet. Biol. 42:119, 2005. (3) Y. Long et al. Plant Pathol. 58:800, 2009. (4) S. X. Zang et al. J. Hebei Normal Univ. Sci. Tech. 19:46, 2005.

Extensive functional diversification of the Populus glutathione S-transferase supergene family

Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.

Molecular characterization of a dehydroascorbate reductase from Pinus bungeana

Abstract Dehydroascorbate reductase (DHAR) plays a critical role in the ascorbate-glutathione recycling reaction for most higher plants. To date, studies on DHAR in higher plants have focused largely on Arabidopsis and agricultural plants, and there is virtually no information on the molecular characteristics of DHAR in gymnosperms. The present study reports the cloning and characteristics of a DHAR (PbDHAR) from a pine, Pinus bungeana Zucc. ex Endl. The PbDHAR gene encodes a protein of 215 amino acid residues with a calculated molecular mass of 24.26 kDa. The predicted 3-D structure of PbDHAR showed a typical glutathione S-transferase fold. Reverse transcription-polymerase chain reaction revealed that the PbDHAR was a constitutive expression gene in P. bungeana. The expression level of PbDHAR mRNA in P. bungeana seedlings did not show significant change under high temperature stress. The recombinant PbDHAR was overexpressed in Escherichia coli following purification with affinity chromatography. The recombinant PbDHAR exhibited enzymatic activity (19.84 micromol/min per mg) and high affinity (a K(m) of 0.08 mM) towards the substrates dehydroascorbate (DHA). Moreover, the recombinant PbDHAR was a thermostable enzyme, and retained 77% of its initial activity at 55 degrees C. The present study is the first to provide a detailed molecular characterization of the DHAR in P. bungeana.

Use of fuzzy evidential reasoning in maritime security assessment

Over the last few years, there has been a growing international recognition that the security performance of the maritime industry needs to be reviewed on an urgent basis. A large number of optional maritime security control measures have been proposed through various regulations and publications in the post-9/11 era. There is a strong need for a sound and generic methodology, which is capable of taking into account multiple selection criteria such as the cost effectiveness of the measures based on reasonable security assessment. The use of traditional risk assessment and decision-making approaches to deal with potential terrorism threats in a maritime security area reveals two major challenges. They are lack of capability of analyzing security in situations of high-level uncertainty and lack of capability of processing diverse data in a utility form suitable as input to a risk inference mechanism. To deal with such difficulties, this article proposes a subjective security-based assessment and management framework using fuzzy evidential reasoning (ER) approaches. Consequently, the framework can be used to assemble and process subjective risk assessment information on different aspects of a maritime transport system from multiple experts in a systematic way. Outputs of this model can also provide decisionmakers with a transparent tool to evaluate maritime security policy options for a specific scenario in a cost-effective manner.

Oily skin: specific features in Chinese women

BACKGROUND/PURPOSE

Inconsistent data are available on the various types of skin, their prevalence and characterization, particularly regarding Asian skins. This observation prompted to conduct a large study in China to assess the prevalence of oily skin and identify the specific factors related to that type of skin.

METHODS

The multicentre trial involved 1787 Chinese women in Shenyang, Harbin, Beijing, Chengdu and Suzhou, between 18 and 65 years of age. Data on history of acne, the presence of environmental factors and a detailed self-evaluation of the skin were collected using a standardized questionnaire. A clinical evaluation of facial skin oiliness was carried-out by a dermatologist at each centre. Sebum secretion was measured on the forehead using Sebumeter SM810. Statistical analysis (multiple correspondence analysis) of typology was conducted based on self-evaluation data.

RESULTS

According to self-evaluation data, oily skin prevalence in the overall Chinese population of the study was 25.6%. Self-evaluation results were quite consistent with sebum measurements and with clinical assessment by dermatologist. Parameters associated with oily skin were (i) shiny skin and a past history of acne, (ii) irregular menstruation, and (iii) highly reactive or sensitive skin. Moreover, a clear and significant link was noted between oily skin and the ingestion of spicy or sweet food. Lastly, sebum levels were found to be twice as high in Beijing as in the other cities and were correlated to higher oily skin prevalence.

CONCLUSION

The study demonstrated the capacity of women for proper self-evaluation of their skin type. It also suggests a potential link between nutritional factors such as spicy and/or sweet diets and oily skin as well as between sensitive and oily skin in this population.

The interaction of Cu2 + ions and NaDC micelles

By mixing an aqueous solution of CuCl2 with an NaDC aqueous solution of various concentration and initial molar ratio, seven coordinated samples with distinct appearances and characters were obtained. Their structures and components were investigated by FT-IR spectroscopy, EXAFS (the extended X-ray absorption fine structure), thermal analysis, X-ray diffraction, laser light scattering, TEM (transmission electron micrograph), element analysis and ICP (inductively coupled plasma) analysis. The following conclusions were given: (1) The complexes of Cu2+-NaDC with distinct appearances and properties were synthesized. (2) After Cu(DC)2 dissolved in NaDC aqueous solution, larger micelles (30-90 nm diameter) formed in the supernate, it is a mixed micelle with Cu(DC)2 and NaDC. So these micelles are a new kind of micelle containing two kinds of metal ions. This is a new result using metal ions as bridges to form micelle. (3) According to the different concentration of Cu2+ to NaDC, the complexes formed as gel or poly-crystals. Both the composition of gel complexes and the coordination structure of carboxyl groups with metal ions varied with the initial molar ratio of Cu2+ to Na+. The gel complexes exhibits the non-stoichiometric character. (4) These results are in agreement with physiological condition. All the different states such as gel, precipitate, micelles of various structures are present in bile of gallbladder. We can suggest an ideal model of the interaction between Cu2+ and bile salts in vivo.

The hemispheric difference of semantic processing of Chinese characters in two dimensions as revealed by ERPs

An experiment was conducted to examine the hemispheric dominance in semantic processing of Chinese characters. Results showed that N1 is the earliest component that reflects the semantic processing of Chinese characters. Although N1 of the left hemisphere is larger in amplitude, that of the right hemisphere is shorter in latency. Based on these findings, the authors propose that the left hemisphere does not start processing until the necessary information has been transferred from the right hemisphere. Once the left hemisphere starts processing, its intensity is stronger. Thus, it is more appropriate to differentiate hemispheric processing dominance into two dimensions: speed and intensity. Moreover, the semantic cognition onset of Chinese characters occurs from 100 ms to 160 ms in the posterior perceptual processing area of brain.

[Energy transfer between electric polymer PVK and terbium complex and its transmission electronmicroscope (TME) study]

A chloroform-soluble terbium complex, which is confirmed to be Tb(aspirin)3 phen using element analysis and FT-IR spectroscopy, was synthesized. Photoluminescent investigation on the terbium complex and PVK-terbium complex composite was conducted. Förster energy transfer occurred between the terbium complex and the PVK matrix. There are no overlap between UV spectrum of the complex and the emission spectrum of PVK, however, overlap is observed between the excitation spectrum of the complex and the emission spectrum of PVK. Therefore, we suggest that the necessary condition of Förster energy transfer should be overlap between the excitation (not UV) spectrum of one complex and the emission spectrum of polymer matrix. Further investigation indicates that the emission of PVK can be suppressed at different extents by doping various amount of Tb(aspirin)3 phen into PVK films. The ratio of Tb(aspirin)3 phen: PVK = 1:2 (wt%) are regarded as an optimized ratio for limiting the emission of PVK. TEM images of PVK/Tb(aspirin)3 phen films reveal that nanoparticles of the Tb complex are dispersed in the PVK matrix. The size of the aggregated complex in PVK matrix is 20-30 nm. The film is not homogeneous as dark regions co-exist with light region in the TEM images. This phenomenon may be related to the short lifetime of electroluminescent devices.

[Systematic study on the authentic and superior medicinal herba and GAP of herba asari]

OBJECTIVE

To investigate the methodology of the systematic study on the Authentic and Superior Medicinal Herba and GAP of Herba Asari.

METHOD

The study was made by textual criticism of Herbology, Botany, Palynology, Cytology, Chemistry, Pharmacology, the analytic methods of allozyme and RAPD. Many subjects on the herb were investigated, such as history, botanical origin, routine examination, morphology of pollen, chromosome and karyotype, the content of oil and its pharmacological effects and so on.

RESULT AND CONCLUSION

The methodology of systematic study on the Authentic and Superior Medicinal Herba was provided. According to the results of the systematic study, the GAP of the herb can be made.

[AFLP markers of restoring genes of the wild-abortive hybrid rice]

Fertile and sterile pools were set up by bulked segregant analysis (BSA) based on the selection for the highly fertile and highly sterile plants of Shanyou 63 F2 population. The AFLP analysis of the two pools indicated that 64 primer combinations amplified 3,477 stable and clear bands. Exception of the combination E-AGC/M-CAA, all primer combinations had not detected polymorphism between the two pools. It was proved by investigation of two parents, individuals of F2 segregant population, backbone sterile lines and restorer lines that the polymorphic fragment AP1 generated from the primer E-AGC/M-CAA was associated with the restoring gene. AP1 was a single copy detected by Southern blot hybridization. The distance between AP1 and the restoring gene was 4.76 cM.

Effects of microinjection of OFQ into PAG on spinal dorsal horn WDR neurons in rats

The aim of the present study was to examine the effect of microinjection of orphanin FQ (OFQ) into periaqueductal gray (PAG) on sensory processing in the wide dynamic range (WDR) neurons of the spinal dorsal horn and to explore the effect of OFQ on a descending system of pain modulation. The results show that microinjection of OFQ into ipsilateral PAG significantly facilitated C-fibre evoked response and post-discharge of spinal dorsal horn WDR neurons. This is consistent with our previous results obtained in behavioral studies. It suggests that the supraspinal effect of OFQ on pain may partly be mediated by PAG neurons.

Expression of 5-HT(1A) receptor mRNA in rat nucleus raphe magnus neurons after peripheral inflammation

The present study demonstrated that 5-HT(1A) receptor mRNA was expressed with moderate level in the NRM neurons. Most of 5-HT(1A) receptor mRNA positive cells were 5-HT neurons, suggesting the majority of 5-HT(1A) receptor in the NRM might be autoreceptors. Eight hours after carrageenan inflammation, the expression of 5-HT(1A) receptor mRNA in the NRM neurons, especially in the 5-HT neurons, was significantly increased. These results suggest that synthesis of 5-HT(1A) receptors, including 5-HT(1A) autoreceptors, is increased in the NRM during peripheral inflammation.

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with homeologous chromosomes 3A and 5A of wheat: the distribution of recombination across chromosomes

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with closely homeologous chromosomes 3A and 5A of T. aestivum was compared with recombination across corresponding homologous chromosome pairs. Differentiation between the homeologues impacted recombination in the proximal regions of the long arms the most and in the distal regions of the long arms the least. It is concluded that this variation principally reflects allocation of multiple crossovers across an arm and positive crossover interference across chromosome arms. Recombination rates between homeologous chromosomes 5A(m) and 5A differed in the opposite sexes.

Position effects of ribosomal RNA multigene loci on meiotic recombination in wheat

Homeologous wheat chromosome arms that differ by the presence or absence of a Nor locus or greatly differ in the numbers of copies of rRNA genes per Nor locus show conspicuous differences in the distribution of recombination. To assess directly the position effects of Nor loci on recombination across chromosome arms, a Triticum monococcum Nor9 haplotype was substituted for Triticum aestivum Nor9 haplotypes on two T. aestivum 1A chromosomes in the isogenic background of cv Chinese Spring. The numbers of rRNA genes in the 1A Nor9 haplotypes are greatly reduced relative to the T. monococcum haplotype. The substitution resulted in reduced recombination rate in the vicinity of the Nor9 locus. An intra-arm compensatory increase was observed in the proximal region of the arm so that the genetic length of the chromosome arm was unchanged. These findings suggest that Nor loci suppress recombination in their vicinity and change recombination patterns in Nor-bearing chromosome arms.

Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species

RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.