Novel electroporation-based genome editing of carnation plant tissues using RNPs targeting the anthocyanidin synthase gene

MAIN CONCLUSION

A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis. As the ANS of 'Kane Ainou 1-go' has not been previously isolated, we initially isolated the ANS gene from 'Kane Ainou 1-go' for characterization. Southern hybridization analysis confirmed that the ANS gene was present in the genome as a two-allele gene with a pair of homologous sequences (ANS-1 and 2); these sequences were used as the target for genome editing. Genome editing was performed by introducing #2_single-guide RNA into the stem tissue using the ribonucleoprotein. This molecule was used because it exhibited the highest efficiency in an analysis of cleavage activity against the target sequence in vitro. Cleaved amplified polymorphic sequence analysis of genomic DNA extracted from 85 regenerated individuals after genome editing was performed. The results indicated that mutations in the ANS gene may have been introduced into two lines. Cloning of the ANS gene in these two lines confirmed the introduction of a single nucleotide substitution mutation for ANS-1 in both lines, and a single amino acid substitution in one line. We discussed the possibility of color change by the amino acid substitution, and also the future applications of this technology.

Identification of genes associated with chlorophyll accumulation in flower petals

Plants have an ability to prevent chlorophyll accumulation, which would mask the bright flower color, in their petals. In contrast, leaves contain substantial amounts of chlorophyll, as it is essential for photosynthesis. The mechanisms of organ-specific chlorophyll accumulation are unknown. To identify factors that determine the chlorophyll content in petals, we compared the expression of genes related to chlorophyll metabolism in different stages of non-green (red and white) petals (very low chlorophyll content), pale-green petals (low chlorophyll content), and leaves (high chlorophyll content) of carnation (Dianthus caryophyllus L.). The expression of many genes encoding chlorophyll biosynthesis enzymes, in particular Mg-chelatase, was lower in non-green petals than in leaves. Non-green petals also showed higher expression of genes involved in chlorophyll degradation, including STAY-GREEN gene and pheophytinase. These data suggest that the absence of chlorophylls in carnation petals may be caused by the low rate of chlorophyll biosynthesis and high rate of degradation. Similar results were obtained by the analysis of Arabidopsis microarray data. In carnation, most genes related to chlorophyll biosynthesis were expressed at similar levels in pale-green petals and leaves, whereas the expression of chlorophyll catabolic genes was higher in pale-green petals than in leaves. Therefore, we hypothesize that the difference in chlorophyll content between non-green and pale-green petals is due to different levels of chlorophyll biosynthesis. Our study provides a basis for future molecular and genetic studies on organ-specific chlorophyll accumulation.

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.)

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. ‘Francesco’ was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp.

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.)

Background

Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F₂ populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research.

Results

We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data.

Conclusions

The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology

Background

Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology.

Results

We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway.

Conclusions

We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

Analysis of genomic DNA of DcACS1, a 1-aminocyclopropane-1-carboxylate synthase gene, expressed in senescing petals of carnation (Dianthus caryophyllus) and its orthologous genes in D. superbus var. longicalycinus

Carnation (Dianthus caryophyllus) flowers exhibit climacteric ethylene production followed by petal wilting, a senescence symptom. DcACS1, which encodes 1-aminocyclopropane-1-carboxylate synthase (ACS), is a gene involved in this phenomenon. We determined the genomic DNA structure of DcACS1 by genomic PCR. In the genome of 'Light Pink Barbara', we found two distinct nucleotide sequences: one corresponding to the gene previously shown as DcACS1, designated here as DcACS1a, and the other novel one designated as DcACS1b. It was revealed that both DcACS1a and DcACS1b have five exons and four introns. These two genes had almost identical nucleotide sequences in exons, but not in some introns and 3'-UTR. Analysis of transcript accumulation revealed that DcACS1b is expressed in senescing petals as well as DcACS1a. Genomic PCR analysis of 32 carnation cultivars showed that most cultivars have only DcACS1a and some have both DcACS1a and DcACS1b. Moreover, we found two DcACS1 orthologous genes with different nucleotide sequences from D. superbus var. longicalycinus, and designated them as DsuACS1a and DsuACS1b. Petals of D. superbus var. longicalycinus produced ethylene in response to exogenous ethylene, accompanying accumulation of DsuACS1 transcripts. These data suggest that climacteric ethylene production in flowers was genetically established before the cultivation of carnation.

Expression of ethylene receptors Dl-ERS1-3 and Dl-ERS2, and ethylene response during flower senescence in Delphinium

To clarify the relationships of flower senescence, especially sepal abscission, and ethylene receptor gene expression in different flower parts, we isolated two cDNAs encoding ethylene receptors Dl-ERS1-3 and Dl-ERS2 from Delphinium flowers. Deduced polypeptides possessed no response regulator domain, indicating that they belong to a family of ethylene response sensor (ERS) ethylene receptors. Dl-ERS1-3 and Dl-ERS2 exhibited constitutive levels during flower senescence. Exogenous ethylene increased transcript levels in sepals, which are influenced by ethylene but not in gynoecia and receptacles, which produce ethylene. It was suggested that expression of ethylene receptor genes under ethylene exposure was differentially regulated in each organ of the flower.

Acetylcholinesterase inhibitor acting on the brain improves detrusor overactivity caused by cerebral infarction in rats

PURPOSE

The functional contribution of the cholinergic pathway in the frontal cortex to micturition was evaluated following cerebral ischemia. Furthermore, it was examined whether reactivation of this regulatory system using acetylcholinesterase inhibitor could improve detrusor overactivity.

METHODS

Left middle cerebral artery occlusion (MCAO) was performed in female Sprague-Dawley rats. Choline acetyltransferase (ChAT) activities after MCAO were assayed to assess the damage to cholinergic neurons. ChAT activities in the bilateral cortex, hippocampus, and pons were calculated by measuring the conversion of 1-[14C] acetyl-coenzyme A to [14C] acetylcholine. Effects on cystometrography of i.v. or i.c.v. donepezil hydrochloride (DON), a centrally acting acetylcholinesterase inhibitor, were investigated in conscious sham-operated (SO) and cerebral infarcted (CI) rats. To investigate whether DON in the forebrain was affected, we decerebrated rats after CI or SO, and investigated the effects on cystometrography of i.v. DON.

RESULTS

Bladder capacity was markedly decreased after MCAO, and remained below half of the pre-occlusion capacity. The greatest increase in bladder capacity was attained at 1.2 x 10(-2) nM/kg of DON given i.v., with a change of 52.8% (P < 0.05). In cases of i.c.v. DON, the greatest increase in bladder capacity was at the dose of 6 x 10(-2) pmol with the change of 95.8% (P < 0.01). The activity of ChAT was decreased in the left cortex and hippocampus 24 h after MCAO (P < 0.05). In decerebrated rats, low dose of DON did not change micturition parameters.

CONCLUSIONS

These results suggest that by upregulation of the forebrain muscarinic inhibitory mechanism, acetylcholinesterase inhibitor improves detrusor overactivity by cerebral infarction.

Purification and characterization of two soluble acid invertase isozymes from Japanese pear fruit

Two isozymes (AIV I and AIV II) of soluble acid invertase (EC 3.2.1.26) were purified from Japanese pear fruit through procedures including (NH(4))(2)SO(4) precipitating, DEAE-Sephacel column chromatography, Concanavalin A (ConA)-Sepharose affinity chromatography, hydroxyapatite column chromatography and Mono Q HR 5/5 column chromatography. The specific activities of purified AIV I and AIV II were 2670 and 2340 (nkat/mg protein), respectively. AIV I was a monomeric enzyme of 80 kDa, while AIV II may be also a monomeric enzyme, which is easy to be cleaved to 52 kDa and 34 kDa polypeptide during preparation by SDS-PAGE. The Km values for sucrose of AIV I and AIV II were 3.33 and 4.58 mM, respectively, and optimum pH of both enzyme activities was pH 4.5.

Changes in the phosphorylation state of sucrose synthase during development of Japanese pear fruit

Changes in the protein level and phosphorylation state of sucrose synthase (SS) were studied throughout the development of Japanese pear fruit. The level of SS protein was high at the young stage, dropped with fruit enlargement and increased again with fruit maturation. Antibody against phospho-Ser reacted with SS from young fruit, but did not react with SS that had been dephosphorylated by alkaline phosphatase (AP). The activities of SS isozymes were separated by ion-exchange chromatography. It was found that the fluctuation in SS activity was caused by two SS isozymes (SSI and SSII); (SSI reacted with antibody against phospho-Ser, while SSII did not. Phosphorylation of SS affected its kinetic parameters, that is, the affinity of phosphorylated SS for UDP was higher than that of dephosphorylated SS, while it was the contrary for UDP-glucose. The reaction of dephosphorylated SS was inclined toward sucrose synthesis more than that of phosphorylated SS. Phosphorylated SS protein was most abundant in young fruit, but decreased with fruit development, while non-phosphorylated SS protein increased in mature fruit. These results suggest that SS isoforms may be affected by post-translational modifications such as phosphorylation, and that the regulation of phosphorylation may potentially control the properties and functions of SS throughout the development of Japanese pear fruit.

FDG PET for evaluating the change of glucose metabolism in prostate cancer after androgen ablation

In the clinical study of prostate cancer, the effect of androgen ablation on glucose metabolism in cancer tissue has not been elucidated. The purpose of this study was to investigate the change in glucose utilization due to endocrine therapy for prostate adenocarcinoma. Ten patients with histologically proven prostate cancer were prospectively investigated with (18)F-fluorodeoxyglucose and positron emission tomography (FDG PET) prior to and after the initiation of endocrine therapy. FDG uptake was calculated to measure glucose utilization in cancer tissue. The change in FDG accumulation was compared with changes in serum prostate specific antigen (PSA) level and prostate size. FDG accumulation in the prostate decreased in all patients 1-5 months after the initiation of hormone therapy. The serum PSA level and prostate size measured on computerized tomography (CT) also decreased in these periods. A decrease in FDG accumulation was also demonstrated in metastatic sites. In this study, there appeared to be a decrease in FDG uptake in prostate cancer after endocrine therapy not only in primary prostate cancer lesions but also at metastatic sites, suggesting that the glucose utilization by tumours was suppressed by androgen ablation.

[A case of renal pelvic tumor with heterotopic bone formation]

The patient was a 74-year-old man who was referred to our hospital with a complaint of left flank pain. Laboratory data were almost within normal limits and urine cytology was positive. X-ray examination revealed a calcification in the left kidney and abdominal CT scan confirmed the presence of a heterogenous renal pelvic mass which contained a calcification. Based on these examinations, a diagnosis of a renal pelvic cancer with heterotopic bone formation was made. Subsequently, left nephroureterectomy was performed. Grossly, the renal pelvis of the resected kidney was filled with a mass which had a white cut surface and bone-like tendency. Histopathologically, a poorly differentiated transitional cell carcinoma with massive bone formation was found. Fifty five cases of heterotopic bone formation in the kidney have been reported in Japan. Among the cases, 4 cases were complicated with renal pelvic tumor and our case was the second case of heterotopic bone formation complicated with a transitional cell carcinoma of the renal pelvis in Japan.

[Two cases of nephrogenic adenoma in the bladder diverticulum]

We report two cases of a nephrogenic adenoma in the bladder diverticulum. The first patient was an 81-year-old man with gross hematuria. Cystoscopy revealed bladder diverticulum and a papillary tumor within. Bladder diverticulectomy was performed and the histopathological diagnosis was a nephrogenic adenoma. The second patient was a 50-year-old man with gross hematuria and dysuria. Transabdominal ultrasound revealed bladder diverticulum. Transurethral coagulation of the bladder diverticulum was performed. Then three papillary tumors were detected, and were resected transurethrally. The histopathological diagnosis was a nephrogenic adenoma. These are the first and second cases of a nephrogenic adenoma in the bladder diverticulum reported in Japan.

[Intra-arterial infusion chemotherapy for liver metastases of testicular tumors: report of two cases]

Two cases of testicular tumors with lymph node involvement and multiple lung and liver metastases were treated successfully with intra-arterial infusion chemotherapy. Case 1: A 30-year-old man presented with right scrotal swelling and an abdominal mass. He had a large retroperitoneal mass and multiple lung and liver metastases on computed tomographic (CT) scan and chest X-ray. Right inguinal orchiectomy was performed. Histopathological diagnosis revealed embryonal cell carcinoma and choriocarcinoma. Cisplatin, vinblastine, VP-16 and pepleomycin combination chemotherapy (PVeBV) was started and repeated for 2 courses. The retroperitoneal mass and lung tumors decreased in size, but liver tumors enlarged. Systemic and intrahepatic arterial infusion combined with chemotherapy was administered, and intra-arterial chemotherapy (cisplatin, VP-16) was added. The patient also received systemic chemotherapy (carboplatin, VP-16, ifosfamide). After chemotherapy, retroperitoneal lymph node dissection was performed. Microscopic examination revealed no viable cancer cells. On CT scan, no retroperitoneal, liver, or lung tumor was detected. Case 2: A 43-year-old man presented with right scrotal swelling and an abdominal mass. CT scan revealed a large retroperitoneal mass as well as lung and multiple liver metastases. Right inguinal orchiectomy was performed. Histopathological diagnosis revealed seminoma. Cisplatin, vinblastine, VP-16 and pepleomycin combination chemotherapy (PVeBV) was administered, but the liver tumors ware enlarged on CT scan. Intrahepatic arterial infusion chemotherapy (cisplatin, VP-16) was started and repeated for 4 courses. On CT scan, the lung metastasis seemed to have disappeared, and the retroperitoneal mass and liver metastases were decreased in size.

Purification and characterization of two sucrose synthase isoforms from Japanese pear fruit

Two isoforms (SS I and SS II) of sucrose synthase (SS; EC 2.54.1.13) were purified from Japanese pear fruit and their properties were compared. SS I mainly appeared in young fruit and SS II mainly in mature fruit. SS I and SS II were purified to the specific activity of 3.37 and 4.26 (units (mg protein)(-1)), respectively. The MW of native and subunit proteins of SS I and SS II were almost the same and both SSs seemed to be a tetramer composed of an 83 kDa polypeptide. However, the ionic charges of the native proteins and the kinetic parameters of SSs were different. Specifically, the Km value for UDP-glucose in SS I was the same as that for UDP, while the Km value for UDP-glucose in SS II was less than that for UDP. SS II easily reacted for sucrose synthesis than sucrose cleavage compared with SS I. Therefore, it is considered that SS I and SS II play different roles in the utilization of carbohydrate in young and mature fruit, respectively.

[Quality of life in patients with testicular cancer after high orchiectomy, radiation therapy or chemotherapy]

We evaluated the physical or psychosocial states of testicular cancer patients receiving orchiectomy, radiation therapy and chemotherapy to assess their quality of life during and after treatment. The subjects were 33 post-treatment patients with testicular cancer who responded to the questionnaire we mailed to them. The quality of life score during chemotherapy showed a decrease, which was accompanied by gastrointestinal symptoms induced by anti-cancer drugs. With regard to the difference in adjuvant treatment types, the surveillance group showed the highest score in the satisfaction of daily life. Moreover, married patients tended to be satisfied with daily life more than non-married patients. With regard to sexual or erectile function, scores of testicular cancer patients, especially in the retroperitoneal lymph node dissection group, were inferior to these of normal volunteers. In conclusion, the physical or psychosocial states after treatment for testicular cancer depend not only on treatment type but also marriage status.

Nephrogenic adenoma in a patient with transitional cell carcinoma of the bladder receiving intravesical bacillus Calmette-Guérin

A 76-year-old-man was admitted to our hospital for a recurrent bladder tumor. He had received intravesical bacillus Calmette-Guérin (BCG) treatment for a transitional cell carcinoma of the bladder. A follow-up cystoscopy revealed a solitary papillary tumor in the left bladder wall. A transurethral cold cup biopsy revealed a nephrogenic adenoma without any evidence of malignant cells. We discuss the pathogenesis of nephrogenic adenoma and suggest that prolonged cystitis caused by intravesical BCG may play an etiological role.

[Retrovesical liposarcoma: a case report]

A case of retrovesical liposarcoma is reported. The patient was a 41-year-old man who complained of left scrotal pain and of hip discomfort. Digital rectal examination revealed a hen's egg-sized mass with an elastic hard consistency at the left side of the normal prostate. Pelvic CT and MRI showed a heterogeneous tumor in the retrovesical region. Transperineal biopsy revealed liposarcoma. Pelvic exenteration, colostomy and ileal conduit were performed. The resected weight was 1,680 grams, and the histopathological diagnosis was myxoid type of liposarcoma, grade II. Postoperatively, a metastatic lesion to vertebrae thoracicae I developed causing radiculoneuropathy of the left superior limb. Spot radiation (50 Gy) was administered to the lesion, but there was no response. Currently, the patient is being treated with combination chemotherapy consisting of dacarbazine, vincristine, adriamycin, and cyclophosphamide. Cases of retrovesical liposarcomas reported in Japan are reviewed and discussed.

[Clinical studies on renal pelvic and ureteral carcinoma]

We reviewed 40 patients with renal pelvic and/or ureteral transitional cell carcinomas, consisting of 24 males and 16 females with a mean age of 65 years. The histopathological stage of surgically removed specimen was pTa in 6 patients, pT1 in 7, pT2 in 5, pT3 in 11 and pT4 in 6. Three patients with Tis and 2 with T3 did not undergo surgery. Of 35 patients pathologically examined, lymphatic and venous invasions were detected in 22 (63%) and 16 (46%), respectively, and were associated with pathological stage and grade. Overall the 5-year actuarial survival rate was 57.1%. Tumor staging and vascular invasion had a prognostic significance on the treatment outcome, but not metachronous or synchronous bladder cancer, identified in 55% of the patients. Adjuvant chemotherapy appeared to improve the survival of the patients with tumors pT2 or higher, grade 3 or vascular invasion without metastases.