Genome-wide identification and analysis of the IQM gene family in soybean.

IQM, a plant-specific calmodulin-binding protein, plays multiple roles in plant growth and development. Although a comprehensive analysis has been carried out on the IQM family genes in Arabidopsis and rice, the number and functions of IQM genes in other species have not been explored. In this study, we identified 15 members of the soybean (Glycine max) IQM gene family using BLASTP tools. These members were distributed on 12 soybean chromosomes and constitute six pairs caused by fragment duplication events. According to phylogeny, the 15 genes were divided into three subfamilies (I, II, and III), and members of the same subfamily had similar gene and protein structures. Yeast two-hybrid experiments revealed that the IQ motif is critical for the binding of GmIQM proteins to GmCaM, and its function is conserved in soybean, Arabidopsis, and rice. Based on real-time PCR, the soybean IQM genes were strongly induced by PEG and NaCl, suggesting their important biological functions in abiotic stress responses. Overall, this genome-wide analysis of the soybean IQM gene family lays a solid theoretical foundation for further research on the functions of GmIQM genes and could serve as a reference for the improvement and breeding of soybean stress resistance traits.

The Calmodulin-Binding Protein IQM1 Interacts with CATALASE2 to Affect Pathogen Defense.

Calmodulin (CaM) regulates plant disease responses through its downstream calmodulin-binding proteins (CaMBPs) often by affecting the biosynthesis or signaling of phytohormones, such as jasmonic acid (JA) and salicylic acid. However, how these CaMBPs mediate plant hormones and other stress resistance-related signaling remains largely unknown. In this study, we conducted analyses in Arabidopsis (Arabidopsis thaliana) on the functions of AtIQM1 (IQ-Motif Containing Protein1), a Ca2+-independent CaMBP, in JA biosynthesis and defense against the necrotrophic pathogen Botrytis cinerea using molecular, biochemical, and genetic analyses. IQM1 directly interacted with and promoted CATALASE2 (CAT2) expression and CAT2 enzyme activity and indirectly increased the activity of the JA biosynthetic enzymes ACX2 and ACX3 through CAT2, thereby positively regulating JA content and B. cinerea resistance. In addition, in vitro assays showed that in the presence of CaM5, IQM1 further enhanced the activity of CAT2, suggesting that CaM5 may affect the activity of CAT2 by combining with IQM1 in the absence of Ca2+ Our data indicate that IQM1 is a key regulatory factor in signaling of plant disease responses mediated by JA. The study also provides new insights that CaMBP may play a critical role in the cross talk of multiple signaling pathways in the context of plant defense processes.

Arabidopsis IQM4, a Novel Calmodulin-Binding Protein, Is Involved With Seed Dormancy and Germination in Arabidopsis.

Seed dormancy and germination are regulated by complex mechanisms controlled by diverse hormones and environmental cues. Abscisic acid (ABA) promotes seed dormancy and inhibits seed germination and post-germination growth. Calmodulin (CaM) signals are involved with the inhibition of ABA during seed germination and seedling growth. In this study, we showed that Arabidopsis thaliana IQM4 could bind with calmodulin 5 (CaM5) both in vitro and in vivo, and that the interaction was the Ca2+-independent type. The IQM4 protein was localized in the chloroplast and the IQM4 gene was expressed in most tissues, especially the embryo and germinated seedlings. The T-DNA insertion mutants of IQM4 exhibited the reduced primary seed dormancy and lower ABA levels compared with wild type seeds. Moreover, IQM4 plays key roles in modulating the responses to ABA, salt, and osmotic stress during seed germination and post-germination growth. T-DNA insertion mutants exhibited ABA-insensitive and salt-hypersensitive phenotypes during seed germination and post-germination growth, whereas IQM4-overexpressing lines had ABA- and osmotic-hypersensitive, and salt-insensitive phenotypes. Gene expression analyses showed that mutation of IQM4 inhibited the expression of ABA biosynthetic genes NCED6 and NCED9, and seed maturation regulators LEC1, LEC2, ABI3, and ABI5 during the silique development, as well as promoted the expression of WRKY40 and inhibited that of ABI5 in ABA-regulated seed germination. These observations suggest that IQM4 is a novel Ca2+-independent CaM-binding protein, which is positively involved with seed dormancy and germination in Arabidopsis.

The progestin norethindrone affects sex differentiation and alters transcriptional profiles of genes along the hypothalamic-pituitary-gonadal and hypothalamic-pituitary-adrenal axes in juvenile zebrafish Dario renio.

Natural and synthetic progestins may pose a threat to wild fish populations living in receiving waters. In this study, the effects of norethindrone (NET) on the sex differentiation of zebrafish (Dario renio) and the mechanisms underlying these effects were investigated. Juvenile zebrafish (20 days post fertilization, pdf) were exposed to environmentally relevant concentrations (5, 50, 500, and 1000 ng L-1) for 45 d. Sex ratio of the NET-exposed populations, the histology of the gonads and the transcriptional profile of the regulatory genes involved in sex differentiation and steroidogenesis were examined. The results showed that a significantly higher ratio of male/female was induced in the zebrafish populations exposed to NET at concentrations higher than 32.3 ng L-1. Exposure to NET caused acceleration of sexual mature in males and a delay in ovary maturation in female zebrafish. Among the genes regulating sexual differentiation, transcripts of Dmrt1 showed a dose-dependent increase while transcripts of Figa and Fox12 showed a dose-dependent decrease in response to exposure to NET. For genes regulating the steroidogenesis, the expressions of Cyp11a1, Cyp17, Cyp19a1a, and Cyp11b were significantly down-regulated by exposure to NET, while Hsd17b3 expression was significantly up-regulated by exposure to NET at 421.3 and 892.9 ng L-1. For the receptor genes in the gonads, the transcriptional expression of Pgr, Ar, and Mr was significantly up-regulated at 421.3 and 892.9 ng L-1 of NET. For genes involved in the hypothalamic-pituitary axis, the transcriptional expression of Gnrh3 and Pomc was significantly up-regulated by exposure to NET with the exception for Gnrh3 at 4.2 ng L-1. The results demonstrated that exposure to NET at the juvenile stage could affect gonad differentiation and sex ratio, which might be accounted for by the alterations of the transcriptional expressions of genes along the hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-adrenal (HPA) axes.

Alterations of secondary sex characteristics, reproductive histology and behaviors by norgestrel in the western mosquitofish (Gambusia affinis).

Synthetic hormones in wastewater effluents released into the aquatic environments may interfere with the normal endocrine systems of fish in receiving streams. Norgestrel (NGT) is a synthetic progestin widely used in oral contraceptives and frequently detected in wastewater effluents. In this study, adult female mosquitofish (Gambusia affinis) were exposed to three environmentally relevant concentrations of norgestrel (NGT) (i.e., 3.6, 35.8, and 368.0 ng L-1) for 42 d, fin morphology, histology of the ovary, and reproductive behaviors were evaluated. The results showed that NGT at all three concentrations caused an increased frequency of atretic follicular cells in ovaries and impaired mating behaviors exhibited by males toward the NGT-exposed females. In mosquitofish exposed to NGT at 35.8 and 368 ng L-1, the anal fin of females had an increased length ratio of ray4/ray 6, an increased width of ray 3, and increased number of segments in ray 3. The histopathological analysis showed that exposure to NGT increased the incidence of spermatogenesis in ovaries. Mating behavior was impaired 58.4%, 65.7%, and 76.4% (P < 0.01 in all cases) when mosquitofish were exposed to NGT at 3.6, 35.6 and 368.0 ng L-1, respectively. The rapid masculinization, the increased frequency of atretic follicles, the incidence of spermatogenesis in the ovary of female fish, and the altered reproductive behaviors suggest that wild populations of mosquitofish could be similarly affected inhabiting in NGT contaminated environments.

Modulation of transcription of genes related to the hypothalamic-pituitary-gonadal and the hypothalamic-pituitary-adrenal axes in zebrafish (Danio rerio) embryos/larvae by androstenedione.

This study aimed to determine the effects of Androstenodione (AED) on the transcriptional expression of genes involved in the hypothalamic-pituitary-gonadal (HPG) and the hypothalamic-pituitary-adrenal (HPA) axes in the zebrafish embryos/larvae. Zebrafish embryos were exposed to 0, 4.0, 45.0, 487.0, and 980.0 ng/L of AED from the day of fertilization to 144 h post fertilization (hpf), during which the transcriptional profiles of key genes related to the HPG and HPA axes were examined daily using quantitative real-time PCR. The AED exposure significantly up-regulated several receptor signaling pathways and the key genes involved in various steps of the steroidogenic pathways were also affected. In addition, the AED exposure could significantly modulate the transcriptional profiles of the other target genes related to hypothalamic and pituitary hormones. The findings of this study suggest that AED, at environmentally relevant concentrations, affects the adrenal endocrine systems and the reproduction of zebrafish by interrupting the HPG and HPA axes.

Research progress on the autonomous flowering time pathway in Arabidopsis.

The transition from vegetative to reproductive growth phase is a pivotal and complicated process in the life cycle of flowering plants which requires a comprehensive response to multiple environmental aspects and endogenous signals. In Arabidopsis, six regulatory flowering time pathways have been defined by their response to distinct cues, namely photoperiod, vernalization, gibberellin, temperature, autonomous and age pathways, respectively. Among these pathways, the autonomous flowering pathway accelerates flowering independently of day length by inhibiting the central flowering repressor FLC. FCA, FLD, FLK, FPA, FVE, FY and LD have been widely known to play crucial roles in this pathway. Recently, AGL28, CK2, DBP1, DRM1, DRM2, ESD4, HDA5, HDA6, PCFS4, PEP, PP2A-B'γ, PRMT5, PRMT10, PRP39-1, REF6, and SYP22 have also been shown to be involved in the autonomous flowering time pathway. This review mainly focuses on FLC RNA processing, chromatin modification of FLC, post-translational modification of FLC and other molecular mechanisms in the autonomous flowering pathway of Arabidopsis.

A simple and efficient genetic transformation method of Ganoderma weberianum.

In this study, the Agrobacterium tumefaciens-mediated transformation method for Ganderma weberianum has been established. Driven by the cauliflower mosaic virus (CaMV) 35S promoter, the hygromycin phosphotransferase (hpt), ß-glucuronidase (uidA), and enhanced green fluorescent protein (egfp) genes have been efficiently expressed in transgenic mycelia and spores. The transformation system was composed of the growing mycelia, A. tumefaciens strain GV3101, and the expression vector pBI-H1, harboring the CaMV 35S promoter and selective hpt marker. The genetic transformation of G. weberianum was achieved through co-cultivation of Agrobacterium lawn and fungal mycelia at 28 °C on yeast extract agar (YEA) medium. Stable genetic transformants were obtained through successive hygromycin B selections and single spore isolation. Over 80 % of transformants showed genetic stability even after ten rounds of subculturing. The simple and efficient genetic transformation method is a useful tool for molecular genetics analyses and gene manipulation of G. weberianum.

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development.

BACKGROUND: Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense. RESULTS: In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development. CONCLUSION: RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.

AtIQM1, a novel calmodulin-binding protein, is involved in stomatal movement in Arabidopsis.

We recently identified a novel IQ motif-containing protein family, IQM, which shares sequence homology with a pea heavy metal-induced protein 6 and a ribosome inactivating protein, trichosanthin. Distinct expression patterns for each gene suggest that each IQM family member may play a different role in plant development and response to environmental cues. However functions of the IQM family members remain to be analyzed. IQM1 bound with calmodulin 5 (CaM5) in yeast two-hybrid assay via its IQ-motif. The CaM binding was Ca(2+)-independent in vitro, and was also observed in bimolecular fluorescence complementation analyses in onion epidermal cells. IQM1 was found to express strongly in guard cells and the cortex of roots. The T-DNA insertion mutants of IQM1 displayed a smaller stomatal aperture, a decreased water loss rate and a shorter primary root. Moreover, iqm1 did not change its stomatal aperture when treated with light, dark, ABA and chitin obviously. Microarray analyses showed that 243 and 28 genes were up- and down-regulated by more than twofold in iqm1-1, respectively. Interesting, 34 of 117 and 7 of 30 chitin-responsive transcriptional factor and ubiquitin ligase genes were up-regulated, respectively. Stomatal guard cells of iqm1-1 also showed enhanced expression of genes involved in production and signaling of reactive oxygen species (ROS). Consistently, increased ROS level was observed in the iqm1 guard cells.

Syntheses, structures and multi-photoluminescence images with confocal microscopy for three 5,5'-azotetrazolate (AZT) based Zn(II) and Ni(II) complexes.

Three 5,5'-azotetrazolate based Zn(II) and Ni(II) complexes exhibit novel supramolecular structures and emit multi-photoluminescence under laser excitation and the multi-photoluminescence promises a multi-channel signal photoluminescent material.

Arabidopsis auxin response factor6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes.

Two mutations in Arabidopsis thaliana, auxin response factor6 (arf6) and arf8, concomitantly delayed the elongation of floral organs and subsequently delayed the opening of flower buds. This phenotype is shared with the jasmonic acid (JA)-deficient mutant dad1, and, indeed, the JA level of arf6 arf8 flower buds was decreased. Among JA biosynthetic genes, the expression level of DAD1 (DEFECTIVE IN ANTHER DEHISCENCE1) was markedly decreased in the double mutant, suggesting that ARF6 and ARF8 are required for activation of DAD1 expression. The double mutant arf6 arf8 also showed other developmental defects in flowers, such as aberrant vascular patterning and lack of epidermal cell differentiation in petals. We found that class 1 KNOX genes were expressed ectopically in the developing floral organs of arf6 arf8, and mutations in any of the class 1 KNOX genes (knat2, knat6, bp and hemizygous stm) partially suppressed the defects in the double mutant. Furthermore, ectopic expression of the STM gene caused a phenotype similar to that of arf6 arf8, including the down-regulation of DAD1 expression. These results suggested that most defects in arf6 arf8 are attributable to abnormal expression of class 1 KNOX genes. The expression of AS1 and AS2 was not affected in arf6 arf8 flowers, and as1 and arf6 arf8 additively increased the expression of class 1 KNOX genes. We concluded that ARF6 and ARF8, in parallel with AS1 and AS2, repress the class 1 KNOX genes in developing floral organs to allow progression of the development of these organs.

[A spectral analysis method for total volatile base nitrogen].

A new method for the determination of the total volatile basic nitrogen (TVB-N) by reflectance spectroscopy was developed. The method was based on the reaction of TVB-N with Nessler's reagent treated by molecular sieve and the reflectance-absorption value F(R), which is directly proportional to the amount of NH2 Hg IO in solid phase, was measured by the reflection spectrometer. The fundamental principle, effective factors and experimental conditions of the method were discussed. The special features of this method were its simplicity in operation, relatively high sensitivity of determination and the use of a small amount of reagent. Linear calibration graph was obtained in the range 1-8 microg x mL(-1) with a detection limit of 0.1 microg x mL(-1). The method was applied to monitor the fresh degree of fish and pork. The result discovered that the total volatile basic nitrogen increased rapidly along with the time extension, indicating that the deterioration of fish and pork was an acceleration process, and the deterioration speed of fish was faster than that of pork.

Changes in growth kinetics of stamen filaments cause inefficient pollination in massugu2, an auxin insensitive, dominant mutant of Arabidopsis thaliana.

We investigated the physiological and molecular basis of lower fecundity of massugu2 (msg2), which is a dominant mutant of an auxin primary response gene, IAA19, in Arabidopsis thaliana. By measuring the length of all stamens and pistils in inflorescences and the reference growth rate of pistils, we constructed growth curves of pistils and stamens between stages 12 and 15 of flower development. Pistil growth was found to consist of a single exponential growth, while stamen growth consisted of three exponential phases. During the second exponential phase, the growth rate of stamen filaments was approximately 10 times greater than the growth rates in the other two phases. Consequently, stamens whose growth was initially retarded grew longer than the pistil, putting pollen grains on the stigma. msg2-1 stamens, on the other hand, exhibited a less obvious growth increase, resulting in less frequent contact between anthers and stigma. MSG2 was expressed in the stamen filaments and its expression almost coincided with the second growth phase. Stamen filaments appeared to elongate by cell elongation rather than cell division in the epidermal cell file. Considering that MSG2 is likely to be a direct target of the auxin F-box receptors, MSG2 may be one of the master genes that control the transient growth increase of stamen filaments.

Molecular cloning and expression analysis of a gene encoding a putative beta-ketoacyl-acyl carrier protein (ACP) synthase III (KAS III) from Jatropha curcas.

A cDNA clone encoding a putative beta-ketoacyl-acyl carrier protein (ACP) synthase III (KAS III) was isolated from Jatropha curcas L., a woody oil plant. The cDNA clone (named JcKAS III) contained a 1203-bp open reading frame coding for 400 amino acids with a predicted molecular mass of about 42 kDa. The deduced amino acid sequence of the cDNA clone shares about 80% identity to KAS III from other plants, and contains a conserved Cys(176) in the active site and the amino acid motif G(355)NTSAAS(361) which is responsible for binding regulatory acyl-ACPs. Southern blotting analysis indicated that JcKAS III is a single copy gene in the J. curcas genome. Quantitative real-time PCR analysis showed that JcKAS III was expressed in all tissues examined with highest expression in roots, and that expression of JcKAS III increased as seeds developed.

Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition.

Auxin response factor (ARF) family genes play a central role in controlling sensitivity to the plant hormone auxin. We characterized the function of ARF8 in Arabidopsis by investigating a T-DNA insertion line (arf8-1) and overexpression lines (ARF8 OX) of ARF8. arf8-1 showed a long-hypocotyl phenotype in either white, blue, red or far-red light conditions, in contrast to ARF8 OX that displayed short hypocotyls in the light. Stronger and weaker apical dominance, and promotion and inhibition of lateral root formation were observed in arf8-1 and ARF8 OX respectively. Sensitivity to auxin was unaltered in arf8-1 hypocotyls with respect to growth inhibition caused by exogenously applied auxin and growth promotion induced by higher temperatures. ARF8 expression was observed constitutively in shoot and root apexes, and was induced in the light condition in hypocotyls. Free IAA contents were approximately 30% reduced in light-grown hypocotyls of ARF8 OX, but were similar between those of arf8-1 and wild type. Expression of the three GH3 genes was reduced in arf8-1 and increased in ARF8 OX, indicating that they are targets of ARF8 transcriptional control. Because the three GH3 proteins may be involved in the conjugation of IAA as suggested by Staswick et al. (2002), and because two of the three GH3 genes are auxin inducible, ARF8 may control the free IAA level in a negative feedback fashion by regulating GH3 gene expression. ARF family genes seem to control both auxin sensitivity and homeostasis in Arabidopsis.

[Teaching reform of hybridization experiment of Drosophila melanogaster].

The paper is concerned about a teaching and learning reform of hybridization experiment of Drosophila melanogaster. In the teaching of genetic experiment, we have adopted a new teaching and learning method which was a discovering way instead of traditional method. In this way, students themselves selected the combination subject, put forward and carried out the whole experiment scheme. By the reform,we could find out that it was helpful not only to improve students' thinking and operating abilities but also to encourage their interests in genetics.