Genome-wide analysis and characterization of Aux/IAA family genes related to fruit ripening in papaya (Carica papaya L.)

Background

Auxin/indole-3-acetic acid (Aux/IAA) family genes encode short-lived nuclear proteins that mediate the responses of auxin-related genes and are involved in several plant developmental and growth processes. However, how Aux/IAA genes function in the fruit development and ripening of papaya (Carica papaya L.) is largely unknown.

Results

In this study, a comprehensive identification and a distinctive expression analysis of 18 C. papaya Aux/IAA (CpIAA) genes were performed using newly updated papaya reference genome data. The Aux/IAA gene family in papaya is slightly smaller than that in Arabidopsis, but all of the phylogenetic subfamilies are represented. Most of the CpIAA genes are responsive to various phytohormones and expressed in a tissues-specific manner. To understand the putative biological functions of the CpIAA genes involved in fruit development and ripening, quantitative real-time PCR was used to test the expression profiling of CpIAA genes at different stages. Furthermore, an IAA treatment significantly delayed the ripening process in papaya fruit at the early stages. The expression changes of CpIAA genes in ACC and 1-MCP treatments suggested a crosstalk between auxin and ethylene during the fruit ripening process of papaya.

Conclusions

Our study provided comprehensive information on the Aux/IAA family in papaya, including gene structures, phylogenetic relationships and expression profiles. The involvement of CpIAA gene expression changes in fruit development and ripening gives us an opportunity to understand the roles of auxin signaling in the maturation of papaya reproductive organs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3722-6) contains supplementary material, which is available to authorized users.

Invited Review Article: Tip modification methods for tip-enhanced Raman spectroscopy (TERS) and colloidal probe technique: A 10 year update (2006-2016) review

Engineering atomic force microscopy tips for reliable tip enhanced Raman spectroscopy (TERS) and colloidal probe technique are becoming routine practices in many labs. In this 10 year update review, various new tip modification methods developed over the past decade are briefly reviewed to help researchers select the appropriate method. The perspective is put in a large context to discuss the opportunities and challenges in this area, including novel combinations of seemingly different methods, potential applications of some methods which were not originally intended for TERS tip fabrication, and the problems of high cost and poor reproducibility of tip fabrication.

Identification, Expression and IAA-Amide Synthetase Activity Analysis of Gretchen Hagen 3 in Papaya Fruit (Carica papaya L.) during Postharvest Process

Auxin plays essential roles in plant development. Gretchen Hagen 3 (GH3) genes belong to a major auxin response gene family and GH3 proteins conjugate a range of acylsubstrates to alter the levels of hormones. Currently, the role of GH3 genes in postharvest physiological regulation of ripening and softening processes in papaya fruit is unclear. In this study, we identified seven CpGH3 genes in a papaya genome database. The CpGH3.1a, CpGH3.1b, CpGH3.5, CpGH3.6, and CpGH3.9 proteins were identified as indole-3-acetic acid (IAA)-specific amido synthetases. We analyzed the changes in IAA-amido synthetase activity using aspartate as a substrate for conjugation and found a large increase (over 5-fold) during the postharvest stages. Ascorbic acid (AsA) application can extend the shelf life of papaya fruit. Our data showed that AsA treatment regulates postharvest fruit maturation processes by promoting endogenous IAA levels. Our findings demonstrate the important role of GH3 genes in the regulation of auxin-associated postharvest physiology in papaya.

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

Sugar apple (Annona squamosa L.) is a semi-deciduous subtropical tree that progressively sheds its leaves in the spring. However, little information is available on the mechanism involved in flower developmental pattern. To gain a global perspective on the floral transition and flower development of sugar apple, cDNA libraries were prepared independently from inflorescent meristem and three flowering stages. Illumina sequencing generated 107,197,488 high quality reads that were assembled into 71,948 unigenes, with an average sequence length of 825.40 bp. Among the unigenes, various transcription factor families involved in floral transition and flower development were elucidated. Furthermore, a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that unigenes exhibiting differential expressions were involved in various phytohormone signal transduction events and circadian rhythms. In addition, 147 unigenes exhibiting sequence similarities to known flowering-related genes from other plants were differentially expressed during flower development. The expression patterns of 20 selected genes were validated using quantitative-PCR. The expression data presented in our study is the most comprehensive dataset available for sugar apple so far and will serve as a resource for investigating the genetics of the flowering process in sugar apple and other Annona species.

Genome-wide identification and characterization of auxin response factor (ARF) family genes related to flower and fruit development in papaya (Carica papaya L.)

Background

Auxin and auxin signaling are involved in a series of developmental processes in plants. Auxin Response Factors (ARFs) is reported to modulate the expression of target genes by binding to auxin response elements (AuxREs) and influence the transcriptional activation of down-stream target genes. However, how ARF genes function in flower development and fruit ripening of papaya (Carica papaya L.) is largely unknown. In this study, a comprehensive characterization and expression profiling analysis of 11 C. papaya ARF (CpARF) genes was performed using the newly updated papaya reference genome data.

Results

We analyzed CpARF expression patterns at different developmental stages. CpARF1, CpARF2, CpARF4, CpARF5, and CpARF10 showed the highest expression at the initial stage of flower development, but decreased during the following developmental stages. CpARF6 expression increased during the developmental process and reached its peak level at the final stage of flower development. The expression of CpARF1 increased significantly during the fruit ripening stages. Many AuxREs were included in the promoters of two ethylene signaling genes (CpETR1 and CpETR2) and three ethylene-synthesis-related genes (CpACS1, CpACS2, and CpACO1), suggesting that CpARFs might be involved in fruit ripening via the regulation of ethylene signaling.

Conclusions

Our study provided comprehensive information on ARF family in papaya, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. The involvement of CpARF gene expression changes in flower and fruit development allowed us to understand the role of ARF-mediated auxin signaling in the maturation of reproductive organs in papaya.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2182-0) contains supplementary material, which is available to authorized users.

An entry to vinylcyclopropane through palladium-catalyzed intramolecular cyclopropanation of alkenes with unstabilized allylic tosylhydrazones

Intramolecular cyclopropanation of unstabilized allylic tosylhydrazones with different alkenes was developed in the presence of a Pd catalyst.

Asymmetric total synthesis of onoseriolide, bolivianine, and isobolivianine

In this article, we describe our efforts on the total synthesis of bolivianine (1) and isobolivianine (2), involving the synthesis of onoseriolide (3). The first generation synthesis of bolivianine was completed in 21 steps by following a chiral resolution strategy. Based on the potential biogenetic relationship between bolivianine (1), onoseriolide (3), and β-(E)-ocimene (8), the second generation synthesis of bolivianine was biomimetically achieved from commercially available (+)-verbenone in 14 steps. The improved total synthesis features an unprecedented palladium-catalyzed intramolecular cyclopropanation through an allylic metal carbene, for the construction of the ABC tricyclic system, and a Diels-Alder/intramolecular hetero-Diels-Alder (DA/IMHDA) cascade for installation of the EFG tricyclic skeleton with the correct stereochemistry. Transformation from bolivianine to isobolivianine was facilitated in the presence of acid. The biosynthetic mechanism and the excellent regio- and endo selectivities in the cascade are well supported by theoretical chemistry based on the DFT calculations.

Bioinspired total synthesis of bolivianine: a Diels-Alder/intramolecular hetero-Diels-Alder cascade approach

We report the first total synthesis of bolivanine in a 14-step pathway involving the synthesis of onoseriolide. Our synthesis features a palladium-catalyzed intramolecular cyclopropanation involving an allylic metal carbene and a Diels-Alder/intramolecular hetero-Diels-Alder cascade, allowing the single-step assembly of a tricyclic system with proper configuration. The synthetic efforts validate our modified biogenetic hypothesis and allow us to confirm the absolute configuration of bolivianine.

Solid state 27Al NMR investigation of Knight shift tensors of LnAl2 (Ln = Y, La and Lu) and correlation with DFT calculations

The atomic and electronic structures of LnAl(2) (Ln=Y, La and Lu) on Al sites were characterized by (27)Al solid state NMR spectroscopy. (27)Al isotropic metallic shifts have been determined in these cubic laves phases under both static and magic angle spinning (MAS) conditions. Based on band structure calculations, we found a strong correlation of (27)Al isotropic metallic shifts and s character of the density of states at the Fermi level on Al sites. We also found tetrahedral distortion of Al centered clusters, which can be well characterized by quadruple coupling constants and Knight shift anisotropy.

NMR signature of evolution of ductile-to-brittle transition in bulk metallic glasses

The mechanical properties of monolithic metallic glasses depend on the structures at atomic or subnanometer scales, while a clear correlation between mechanical behavior and structures has not been well established in such amorphous materials. In this work, we find a clear correlation of (27)Al NMR isotropic shifts with a microalloying induced ductile-to-brittle transition at ambient temperature in bulk metallic glasses, which indicates that the (27)Al NMR isotropic shift can be regarded as a structural signature to characterize plasticity for this metallic glass system. The study provides a compelling approach for investigating and understanding the mechanical properties of metallic glasses from the point of view of electronic structure.

Total synthesis of (±)-chloranthalactone A

A total synthesis of (±)-chloranthalactone A was completed. It features substrate-controlled epoxidation of ketone and highly diastereoselective intramolecular cyclopropanation to construct the cis, trans-3/5/6 tricyclic skeleton.

Isolation and characterization of phenolic compounds from the leaves of Salix matsudana

A bioassay-guided in vitro screen has revealed that a 70% methanol extract of the leaves of Salix matsudana shows considerable inhibitory activity against cyclooxygenases (COX-1 and COX-2). A subsequent phytochemical study led to the isolation of a new flavonoid, matsudone A (1), together with five known flavonoids--luteolin (2), isoquercitrin (3), 7-methoxyflavone (4), luteolin 7-O-glucoside (5), 4',7-dihydroxyflavone (6)--and two phenolic glycosides, leonuriside A (7) and piceoside (8). Their structures were elucidated on the basis of extensive 1D- and 2D-NMR studies, high resolution ESI mass spectroscopic analyses and comparisons with literature data. The isolated compounds 1-8 were tested for their inhibitory activities against COX-1 and COX-2. Compounds 1, 5 and 6 were found to have potent inhibitory effect on COX-2 and compounds 3-5 exhibited moderate inhibition against COX-1.

Whole-body positron emission tomography with 18F-fluorodeoxyglucose is an effective method to detect extra-pelvic recurrence in uterine sarcomas

PURPOSE OF INVESTIGATION

To assess the clinical use of F-18-fluorodeoxyglucose positron emission tomography (FDG-PET) in the post-therapy surveillance of uterine sarcoma.

METHODS

Eight whole-body FDG-PET studies were performed in seven women with previously treated uterine sarcoma. Conventional image studies (computed tomography) and physical examinations were performed for follow-up. All FDG-PET studies were indicated to localize suspected recurrences noted by conventional methods.

RESULTS

The per case sensitivity of the FDG-PET studies and CT scans was 85.7% (6/7) and 100% (7/7), respectively (p = 0.174). FDG-PET was able to detect seven extrapelvic metastastic sites below the diaphragm (7/7, sensitivity: 100%), including the liver, spleen, paraaortic lymph node, spine and paracolic gutter, as well as pulmonary lesions in five patients, while the CT scan detected only three lesions (3/7, sensitivity: 42.9%; p = 0.070). FDG-PET detected only four recurrent pelvic lesions (4/6) and CT scan detected six (6/6) recurrent pelvic lesions (66.7% vs 100%, p = 0.455).

CONCLUSIONS

The FDG-PET showed a better detection rate than the abdominal CT scan for extrapelvic metastatic lesions and a similar detection rate as well as abdominal CT scan. FDG-PET can serve as a useful detection tool for patients with uterine sarcomas because nearly 80% of recurrence involve an extrapelvic site.

Autofluorescence reveals menstrual phase in the endometrium

OBJECTIVE

Tissue contains fluorophores that autofluoresce without additional dye or photosensitizer with the appropriate light excitation. This technique has been widely applied for discrimination between normal and precancerous tissue. The aim of this study was to explore the capability and reliability of autofluorescence phase determination in samples of human endometrium.

METHODS

A total of 70 measurement sites from 31 endometrial tissue samples from hysterectomy were enrolled. Xenon light (330 nm) was directed at the endometrial tissue and the resultant autofluorescence intensity recorded. Spectra were then grouped according to the proliferative and secretory phase, with multivariant analysis, partial least square (PLS) and analysis of variance (ANOVA) used for evaluation of the statistical significance of phase determination.

RESULTS

Both proliferative and secretory autofluorescence spectra showed a similar characteristic triple-peak curve shape pattern, however, each of the intensities at the three peaks between the two phases varied markedly (p < 0.01). PLS analysis confirmed that collagen, NADH and FAD autofluorescence were the principle determinants of endometrial spectrum; the sensitivity and specificity of phase determination by autofluorescent was 100% and 97%, respectively.

CONCLUSION

Autofluorescence measurement provides real-time information on endometrial phase status and, based on our results, it appears reasonable to suggest that it may be promising as a clinical tool for prompt phase interpretation.

Presumed Stage IA primary epithelial ovarian carcinoma: the role of complete staging surgery

PURPOSE

Proper staging is warranted in any patient with primary epithelial ovarian carcinoma (PEOC), but sometimes it cannot always be performed. The prognosis of patients with and without complete staging surgery is to be determined.

METHODS

We retrospectively evaluated 61 patients with presumed Stage IA PEOC between January 1970 and December 1993. Inclusion criteria were: being referred patients; no ascites; an intact ovarian tumor without extra-spillage or rupture before, during or after operation; conventional regular exploratory laparotomy without urgency; more than a 5-year follow-up, except for recurrent diseases; a detailed pathology review; and no other systemic disease. Tumors of lower malignant potential (LMP) and cystectomy for removing tumor were excluded. Of the 61 patients, 17 patients received a close observation (Group A), and the others (44 patients) received a re-exploratory laparotomy to complete the staging surgery (Group B).

RESULTS

The mean follow-up time was 7.4 years, ranging between 5.4 and 11.1 years, in Group A, and 8.1 years, ranging from 5.6 to 12.7 years, in Group B. Two patients (11.8%) in Group A and seven patients (15.9%) in Group B suffered from recurrence. Two patients finally died of disease, and both were in Group B.

CONCLUSIONS

Based on the observation in this study that the recurrence rate of the two groups was not statistically different, close follow-up for patients with presumed Stage IA EOC, but without complete surgical staging surgery, might be acceptable when these patients are treated with postoperative adjuvant chemotherapy.

Radical hysterectomy: past, present, and future

After an analysis of 3,441 radical hysterectomies performed in our department, we found, after modification of the operative technique in 1983, the more lateral the excision the less the recurrence rate. The recurrence rate for Stage 1b-2a and Stage 2b patients comparing the years before 1983 to the years after decreased to 12.4% from 15.7% (158/1,006 vs 268/2,163; p = 0.009) in Stage 1b-2a and 24.6% from 55.8% (38/68 vs 47/191; p = 0.0007) in Stage 2b, respectively. With the modern trend of aspiring for an easier lifestyle, most physicians practice earlier. Therefore only very few physicians study radical hysterectomy. As the skill of surgery needs a longer period of education and training, it may only interest physicians who work with medical professionals as part of a team at a medical center. In the future, we should provide gynecological residents not only with a training program using the classic textbooks, but also with different points of view on changes and developments in radical hysterectomy. We hope to promote an attitude of offering patients access to different choices and opportunities of therapy. Radical hysterectomy is in fact a treatment option for patients with bulky cervical lesions and Stage 2b in particular.

Cytokeratin-19 associated with apoptosis and chemosensitivity in human cervical cancer cells

Cytokeratins are one group of intermediate filament proteins responsible for the integrity of cell structure, and have been recently reported to play a role in conferring a drug resistance phenotype. MAb Cx-99 is a monoclonal antibody exhibiting the specificity toward its corresponding antigen which was recently identified as the cytokeratin-19 protein. In the present study, we found that the level of cytokeratin-19 in cervical cancer cells could be decreased by incubation of cancer cells with MAb Cx-99. The reduction of cytokeratin-19 level had a killing effect on cervical carcinoma SIHA and HeLa S3 cell lines. The DNA ladder pattern, convoluted nuclei and blebbing morphology were observed with these cells after exposure to MAb Cx-99 for 72 h, suggesting that the cytotoxic mechanism of reduced cytokeratin-19 was mediated by induction of apoptosis. Moreover, the MAb Cx-99 treatment could increase the cytotoxicities of cancer chemotherapeutic agents such as cisplatin and vinblastine to both cervical carcinoma cell lines. The LD80 values were at least 15-fold reduced when cancer cells were treated with cisplatin or vinblastine in the presence of MAb Cx-99. These results suggest that the functional role of cytokeratin-19 was associated with the apoptosis prevention and drug resistance of cervical cancer cells.