Post-RFA Pulmonary Vein Stenosis Mimicking Lymphangitic Carcinomatosis in a Patient With History of Liposarcoma.

ABSTRACT: A 58-year-old man with resected liposarcoma exhibited persistent irregular interlobular septal thickening of lung on CT concerning lymphangitic metastasis. FDG PET/CT was positive in these foci. There was a narrowing of the pulmonary veins, which had not been seen on the imaging conducted prior to radiofrequency ablation therapy for atrial fibrillation. Lung perfusion scanning demonstrated more extensive hypoperfusion. This case highlights the diagnostic pitfalls of interstitial thickening of the lung in cancer patients. Meticulous history review and nuclear imaging helped distinguish the postablation pulmonary venous stenosis from metastatic spread to the lung interstitium.

Prognostic impact of 18F-FDG PET/CT in pathologic stage II invasive ductal carcinoma of the breast: re-illuminating the value of PET/CT in intermediate-risk breast cancer.

BACKGROUND: The aim of this study is to investigate the impact of 18F-FDG PET/CT on prognosis of stage II invasive ductal carcinoma (IDC) of the breast primarily treated with surgery. METHODS: The clinical records of 297 consecutive IDC with preoperative PET/CT and pathologically staged II in surgery from 2013 to 2017 were retrospectively reviewed. The maximum standardized uptake value (SUVmax), peak standardized uptake value (SUVpeak), tumor-to-liver ratio (TLR), and metabolic tumor volume (MTV) were measured. Association of clinicopathologic factors (age, T stage, N stage, AJCC pathologic stage of IIA or IIB, pathologic prognostic stage, grade, hormonal receptor status, HER2 status, Ki-67, and adjuvant therapy) and PET parameters with DFS was assessed using the Cox proportional hazards model. RESULTS: There were 35 recurrences and 10 deaths at a median follow-up of 49 months (range 0.8 ~ 87.3). All PET parameters were significantly associated with DFS in univariate analysis but in multivariate analysis, SUVpeak was the only factor significantly associated with DFS (hazard ratio 2.58, 95% confidence interval 1.29-5.15, P = 0.007). In cohorts with higher values of SUVpeak or TLR, patients who received adjuvant chemotherapy had significantly superior DFS. CONCLUSION: Metabolic parameters derived from preoperative PET/CT was significantly associated with recurrence in stage II IDC primarily treated with surgery. PET/CT can be a powerful prognostic tool in conjunction with novel staging systems and current biomarkers for patients undergoing contemporary therapy. Our results urge to reconsider the currently underestimated value of PET/CT confined to diagnostic aspect and to newly recognize its prognostic impact in these intermediate-risk breast cancer.

Comparison of early F-18 Florbetaben PET/CT to Tc-99m ECD SPECT using voxel, regional, and network analysis.

This study aimed to validate early-phase F-18 Florbetaben positron emission tomography (eFBB PET) as a brain perfusion test and determine the optimal reference region. A total of 27 patients with early Parkinson's disease with Tc-99m ethyl cysteinate dimer single photon emission tomography (ECD SPECT) and FBB PET were included. Six reference regions, including whole brain (GN), pons, central white matter (CWM), whole cerebellum (WC), WC with brain stem (WC + B), and cerebellar grey matter (CG), were applied to obtain SUVR using cortex volume-of-interest (VOI). Reference regions of WC (r 0.886), WC + B (r 0.897), and CG (r 0.904) had highest correlation values of cortex-VOI SUVR between both perfusion images (all p < 0.001). Early-phase FBB PET had a significant linear correlation of CG-normalized SUVR of the cortex, basal ganglia, thalamus, and midbrain with ECD SPECT in voxel-wise analysis (FDR adjusted-p < 0.05). Early-phase FBB PET extracts more ICNS than ECD SPECT, as 9 ICNS and 4 ICNs, respectively. Both eFBB PET and ECD SPECT well discriminated PD from DLB (Area-under-curve of receiver-operating-characteristics, 0.911 for eFBB PET, 0.922 for ECD SPECT). Our findings suggest that eFBB PET is a reliable perfusion test based on a high correlation with ECD SPECT using cerebellum-based normalization methods.

One Versus Up-to-5 Lesion Measurements for Response Assessment by PERCIST in Patients with Lung Cancer.

PURPOSE: The optimal number of lesions to measure for response assessment from fluorine-18 fluorodeoxyglucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) is not validated for lung cancer. We compared 1 lesion and up-to-5 lesion measurements for response assessment in lung cancer per PET Response Criteria in Solid Tumors (PERCIST). METHODS: Patients with lung cancer with pre- and post-treatment PET/CT images were included. The standard uptake value corrected for lean body mass (SULpeak) of up-to-5 hottest target lesions was measured at each time point. The percent changes of SULpeak of the single hottest lesion and the sum of up-to-5 hottest lesions were computed. Pearson correlation coefficient evaluated the strength of association between the percent changes of SULpeak values from the 1 lesion and up-to-5 lesion analyses. Response categories were complete metabolic response (CMR) with no perceptible lesion; partial metabolic response (PMR), stable metabolic disease (SMD), or progressive metabolic disease (PMD) using the threshold of 30% and 0.8 unit change in SULpeak; and unequivocal new lesion meant PMD. The concordance for response categorization was assessed by kappa statistics. RESULTS: A total of 40 patients (25 non-small cell lung cancer; 15 small cell lung cancer) were analyzed, all with 18F-FDG-avid lung cancer. Average of 3 target lesions were measured for up-to-5 lesion analysis. Pearson's r was 0.74 (P < 0.001) and increased to 0.96 (P < 0.001) when two outliers were excluded. Response categorization with 1 lesion and up-to-5 lesion analyses was concordant in 37 patients (92.5%, weighted kappa = 0.89). CONCLUSION: Analyzing 1 lesion and up-to-5 lesions for response assessment by PERCIST showed high concordance in patients with lung cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13139-021-00697-4.

Prognostic value of tumor metabolic imaging phenotype by FDG PET radiomics in HNSCC.

OBJECTIVE: Tumor metabolic phenotype can be assessed with integrated image pattern analysis of 18F-fluoro-deoxy-glucose (FDG) Positron Emission Tomography/Computed Tomography (PET/CT), called radiomics. This study was performed to assess the prognostic value of radiomics PET parameters in head and neck squamous cell carcinoma (HNSCC) patients. METHODS: 18F-fluoro-deoxy-glucose (FDG) PET/CT data of 215 patients from HNSCC collection free database in The Cancer Imaging Archive (TCIA), and 122 patients in Seoul St. Mary's Hospital with baseline FDG PET/CT for locally advanced HNSCC were reviewed. Data from TCIA database were used as a training cohort, and data from Seoul St. Mary's Hospital as a validation cohort. With the training cohort, primary tumors were segmented by Nestles' adaptive thresholding method. Segmental tumors in PET images were preprocessed using relative resampling of 64 bins. Forty-two PET parameters, including conventional parameters and texture parameters, were measured. Binary groups of homogeneous imaging phenotypes, clustered by K-means method, were compared for overall survival (OS) and disease-free survival (DFS) by log-rank test. Selected individual radiomics parameters were tested along with clinical factors, including age and sex, by Cox-regression test for OS and DFS, and the significant parameters were tested with multivariate analysis. Significant parameters on multivariate analysis were again tested with multivariate analysis in the validation cohort. RESULTS: A total of 119 patients, 70 from training, and 49 from validation cohort, were included in the study. The median follow-up period was 62 and 52 months for the training and the validation cohort, respectively. In the training cohort. binary groups with different metabolic radiomics phenotypes showed significant difference in OS (p = 0.036), and borderline difference in DFS (p = 0.086). Gray-Level Non-Uniformity for zone (GLNUGLZLM) was the most significant prognostic factor for both OS (hazard ratio [HR] 3.1, 95% confidence interval [CI] 1.4-7.3, p = 0.008) and DFS (HR 4.5, CI 1.3-16, p = 0.020). Multivariate analysis revealed GLNUGLZLM as an independent prognostic factor for OS (HR 3.7, 95% CI 1.1-7.5, p = 0.032). GLNUGLZLM remained as an independent prognostic factor in the validation cohort (HR 14.8. 95% CI 3.3-66, p < 0.001). CONCLUSIONS: Baseline FDG PET radiomics contain risk information for survival prognosis in HNSCC patients. The metabolic heterogeneity parameter, GLNUGLZLM, may assist clinicians in patient risk assessment as a feasible prognostic factor.

Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant.

Triterpenoid saponins (TSs) are common plant defense phytochemicals with potential pharmaceutical properties. Platycodon grandiflorus (Campanulaceae) has been traditionally used to treat bronchitis and asthma in East Asia. The oleanane-type TSs, platycosides, are a major component of the P. grandiflorus root extract. Recent studies show that platycosides exhibit anti-inflammatory, antiobesity, anticancer, antiviral, and antiallergy properties. However, the evolutionary history of platycoside biosynthesis genes remains unknown. In this study, we sequenced the genome of P. grandiflorus and investigated the genes involved in platycoside biosynthesis. The draft genome of P. grandiflorus is 680.1 Mb long and contains 40,017 protein-coding genes. Genomic analysis revealed that the CYP716 family genes play a major role in platycoside oxidation. The CYP716 gene family of P. grandiflorus was much larger than that of other Asterid species. Orthologous gene annotation also revealed the expansion of ß-amyrin synthases (bASs) in P. grandiflorus, which was confirmed by tissue-specific gene expression. In these expanded gene families, we identified key genes showing preferential expression in roots and association with platycoside biosynthesis. In addition, whole-genome bisulfite sequencing showed that CYP716 and bAS genes are hypomethylated in P. grandiflorus, suggesting that epigenetic modification of these two gene families affects platycoside biosynthesis. Thus whole-genome, transcriptome, and methylome data of P. grandiflorus provide novel insights into the regulation of platycoside biosynthesis by CYP716 and bAS gene families.

Predictive Value of Interim and End-of-Therapy 18F-FDG PET/CT in Patients with Follicular Lymphoma.

PURPOSE: 18F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) is the standard imaging modality for response evaluation in FDG-avid lymphoma, but the prognostic value is not established in follicular lymphoma (FL). This study investigated the prognostic value of Deauville 5-point scale (D5PS) from paired interim PET/CT (PETInterim) and end-of-induction therapy PET/CT (PETEOI) in patients with FL. METHODS: FL staging and response assessment PET/CT images from 2013 to 2015 were retrospectively reviewed. PETInterim was performed 3 or 4 cycles after chemotherapy and PETEOI after 6 or 8 cycles. D5PS scores of 1, 2, and 3 were considered as negative (-), and scores 4 and 5 were considered as positive (+). Statistical analysis was done using Cox regression analysis, Kaplan-Meier survival analysis, and the log-rank test. RESULTS: Thirty-three patients with set of baseline, interim, and end-of-induction therapy PET/CT studies were included. Ten patients (30.3%) had progression. The median progression-free survival (PFS) was 38.8 months (range 3.5-72.7 months). On PETInterim, 23 patients were negative and 10 were positive. On PETEOI scans, 29 patients were negative, and 4 were positive. On multivariate analysis, PETEOI(-) was associated with longer PFS. PETInterim(+) and PETEOI(+) patients had a significantly shorter PFS than PETInterim(-) patients (39.9 months, 95% confidence interval [CI] 23.0-56.9, versus 55.5 months, 95% CI 49.7-61.2, p = 0.005) and PETEOI(-) patients (14.2 months, 95% CI 8.5-19.8, versus 60.5 months, 95% CI 52.1-69.0, p < 0.001). CONCLUSION: For patients with FL, PETInterim and PETEOI response is predictive of PFS, and PETEOI(+) is an independent prognostic factor for progression of FL.

Cerebrospinal fluid from Alzheimer's disease patients as an optimal formulation for therapeutic application of mesenchymal stem cells in Alzheimer's disease.

Mesenchymal stem cells (MSCs) have emerged as one of the promising treatment options for Alzheimer's disease (AD). Although many studies have investigated on the efficacy of MSCs in AD, how MSCs actually change following exposure to the AD environment has not been studied extensively. In this study, we investigated on the potential of AD patient-cerebrospinal fluid (CSF) samples to be used as a formulation of MSCs and its application in AD therapeutics. When Wharton's jelly-derived mesenchymal stem cells (WJ-MSCs) were stored in the CSF of AD patients, the stemness of WJ-MSCs was preserved. Furthermore, several genes were upregulated following storage in AD CSF. This signified the therapeutic potential of CSF formulation for AD therapy. Overall, these findings suggest that CSF from AD patients can be an optimal source for MSC formulation.

Selective Production of p-Xylene from Dimethylfuran and Ethylene Over Tungstated Zirconia Catalysts.

p-Xylene (PX) is an important large-volume commodity chemical in the petrochemical industry. Therefore, research on producing PX from bio-mass-derived resources is a considerable interest in relation to future alternative technologies. Recently, a new potential route for the direct and selective production of bio-based PX was reported, referred to as the Diels-Alder cycloaddition of biomassderived 2,5-dimethylfuran (DMF) and ethylene followed by the dehydration of an intermediate. Here, we prepared tungstated zirconia (WOx-ZrO2) materials at different calcination temperatures and times as solid acid catalysts for PX production. From structural analyses and measurements of the surface acidity, the WOx-ZrO2 was found to be composed of mesopores with high surface acidity within the optimum calcination temperature and time range. This WOx-ZrO2 catalyst exhibited high catalytic activity upon the cycloaddition of DMF with ethylene as compared to commercial beta zeolite and previously reported silica-alumina catalysts.

Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild Chrysanthemum species.

KEY MESSAGE: Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.

Agouti Related Peptide Secreted Via Human Mesenchymal Stem Cells Upregulates Proteasome Activity in an Alzheimer's Disease Model.

The activity of the ubiquitin proteasome system (UPS) is downregulated in aggregation diseases such as Alzheimer's disease (AD). In this study, we investigated the therapeutic potential of the Agouti-related peptide (AgRP), which is secreted by human mesenchymal stem cells (MSCs), in terms of its effect on the regulation of proteasome activity in AD. When SH-SY5Y human neuroblastoma cells were co-cultured with MSCs isolated from human Wharton's Jelly (WJ-MSC), their proteasome activity was significantly upregulated. Further analysis of the conditioned media after co-culture allowed us to identify significant concentrations of a neuropeptide, called AgRP. The stereotactic delivery of either WJ-MSCs or AgRP into the hippocampi of C57BL6/J and 5XFAD mice induced a significant increase of proteasome activity and suppressed the accumulation of ubiquitin-conjugated proteins. Collectively, these findings suggest strong therapeutic potential for WJ-MSCs and AgRP to enhance proteasome activity, thereby potentially reducing abnormal protein aggregation and delaying the clinical progression of various neurodegenerative diseases.

Licoricidin, an Active Compound in the Hexane/Ethanol Extract of Glycyrrhiza uralensis, Inhibits Lung Metastasis of 4T1 Murine Mammary Carcinoma Cells.

Licorice extracts containing glycyrrhizin exhibit anti-carcinogenic properties. Because glycyrrhizin induces severe hypokalemia and hypertension, we prepared a hexane/ethanol extract of Glycyrrhiza uralensis (HEGU) that lacks glycyrrhizin, and showed that HEGU induces apoptosis and G1 cell cycle arrest and inhibits migration of DU145 human prostate cancer cells. Our previous in vitro studies identified two active components in HEGU: isoangustone A, which induces apoptosis and G1 cycle arrest, and licoricidin, which inhibits metastasis. This study examined whether HEGU and licoricidin inhibit metastasis using the 4T1 mammary cancer model. Both HEGU and licoricidin treatment reduced pulmonary metastasis and the expression of CD45, CD31, HIF-1α, iNOS, COX-2, and VEGF-A in tumor tissues. Additionally, a decrease in protein expression of VEGF-R2, VEGF-C, VEGF-R3, and LYVE-1 was noted in tumor tissues of licoricidin-treated mice. Furthermore, the blood concentrations of MMP-9, ICAM-1, VCAM-1, and VEGF-A were decreased in HEGU-treated mice. In vitro 4T1 cell culture results showed that both HEGU and licoricidin inhibited cell migration, MMP-9 secretion, and VCAM expression. The present study demonstrates that the licoricidin in HEGU inhibits lung metastasis of 4T1 mammary carcinoma cells, which may be mediated via inhibition of cancer cell migration, tumor angiogenesis, and lymphangiogenesis.

Licochalcone E present in licorice suppresses lung metastasis in the 4T1 mammary orthotopic cancer model.

We investigated whether licochalcone E (LicE), a phenolic constituent of licorice, inhibits mammary tumor growth and metastasis using animal and cell culture models. 4T1 mammary carcinoma cells were injected into the mammary fat pads of syngeneic BALB/c mice. Starting 7 days after the injection, the mice received LicE (7 or 14 mg/kg body weight/day) via oral gavage for 25 days. LicE suppressed solid tumor growth and lung metastasis, but did not exhibit kidney or liver toxicity. In tumor tissues, LicE treatment induced a reduction in the expression of Ki67, cyclins, and cyclin-dependent kinases and stimulated apoptosis with increased expression of Bax and cleaved caspase-3 but decreased expression of Bcl-2. In addition, LicE decreased expression of CD31, vascular endothelial growth factor (VEGF)-A and C, VEGF-receptor 2, lymphatic vessel endothelial receptor-1, CD45, cyclooxygenase-2, inducible nitric oxide synthase, and hypoxia inducible factor-1α in tumor tissues. In lung tissues, LicE reduced the levels of proinflammatory cytokines and angiogenesis/metastasis-related proteins. In mammary cancer cell cultures, LicE (5-20 µmol/L) dose dependently inhibited cell migration and invasion. LicE inhibited secretion of matrix metalloproteinase-9, urokinase-type plasminogen activator and VEGF-A, and stimulated secretion of tissue inhibitor of metalloproteinase-2 in MDA-MB-231 cells. In addition, LicE inhibited tube formation of vascular endothelial cells. We show that LicE administration suppressed tumor growth and lung metastasis in the mouse model in conjunction with LicE inhibition of cell migration, invasion, and tube formation in vitro. Reduced tumor growth and metastasis in LicE-treated mice may be, at least in part, attributed to reduced inflammation and tumor angiogenesis.

Hexane/ethanol extract of Glycyrrhiza uralensis and its active compound isoangustone A induce G1 cycle arrest in DU145 human prostate and 4T1 murine mammary cancer cells.

Although licorice is known to exert anticarcinogenic effects, it contains large quantities of glycyrrhizin (GL), which causes severe hypertension. We have previously demonstrated that the hexane/ethanol extract of Glycyrrhiza uralensis (HEGU) contains no detectable GL and suppresses doxorubicin-induced apoptosis in H9c2 rat cardiac myoblasts. The principal objective of this study was to determine whether and by what mechanism HEGU and its active component, isoangustone A, inhibit cell-cycle progression in DU145 human prostate and 4T1 mouse breast cancer cells. HEGU and isoangustone A dose-dependently decreased DNA synthesis and induced G1 phase arrest in both DU145 and 4T1 cells. HEGU and isoangustone A reduced the levels of CDK2 and CDK4 as well as cyclin A and cyclin D1 proteins, and also induced a decrease in CDK2 activity. The addition of HEGU to drinking water significantly suppressed the orthotopic growth of 4T1 allografts and the expression of the proliferating nuclear cell antigen, CDK2 and CDK4 proteins in the tumor tissues. These results demonstrate the potential of HEGU containing isoangustone A as an antitumor agent.

RAGE ligands induce apoptotic cell death of pancreatic ß-cells via oxidative stress.

Activation of the receptor for advanced glycation endproducts (RAGE) by its ligands leads to cellular damage contributing to diabetic complications. It is not clearly known whether RAGE ligands influence pancreatic ß-cells. In this study, we investigated the expression of RAGE in islet cells and the effect of RAGE ligands, S100b and HMG-1, on islet cells. RAGE was expressed in INS-1 cells and isolated rat and human islets at mRNA and protein levels. RAGE and its ligand, S100b, were detected on islet cells in 28-week-old diabetic OLETF rats. Both S100b and HMG-1 induced apoptotic cell death of INS-1 and islet cells. This INS-1 cell apoptosis was accompanied by increased intracellular oxidative stress and inhibited by antioxidants or a NADPH oxidase inhibitor. Our results showing S100b/RAGE expression on islets of diabetic rat model and RAGE ligands-induced islet cell apoptosis via NADPH oxidase-mediated ROS generation suggest that RAGE ligands-RAGE interaction may contribute not only to the development of diabetic complications but also to the progressive ß-cell loss in type 2 diabetes by inducing oxidative stress.

Sequence and structure of Brassica rapa chromosome A3.

BACKGROUND: The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species. RESULTS: We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3. CONCLUSIONS: We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.

Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis.

BACKGROUND: The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level. RESULTS: We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events. CONCLUSION: Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions of genes in B. rapa based on the locations of orthologues in A. thaliana can be misleading. Our results will be of relevance to a wide range of plants that have polyploid genomes, many of which are being considered according to a paradigm of comprising conserved synteny blocks with respect to sequenced, related genomes.

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.

BACKGROUND: Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. RESULTS: We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. CONCLUSIONS: This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.

Genome-wide identification of glucosinolate synthesis genes in Brassica rapa.

Glucosinolates play important roles in plant defense against herbivores and microbes, as well as in human nutrition. Some glucosinolate-derived isothiocyanate and nitrile compounds have been clinically proven for their anticarcinogenic activity. To better understand glucosinolate biosynthesis in Brassica rapa, we conducted a comparative genomics study with Arabidopsis thaliana and identified total 56 putative biosynthetic and regulator genes. This established a high colinearity in the glucosinolate biosynthesis pathway between Arabidopsis and B. rapa. Glucosinolate genes in B. rapa share 72-94% nucleotide sequence identity with the Arabidopsis orthologs and exist in different copy numbers. The exon/intron split pattern of B. rapa is almost identical to that of Arabidopsis, although inversion, insertion, deletion and intron size variations commonly occur. Four genes appear to be nonfunctional as a result of the presence of a frame shift mutation and retrotransposon insertion. At least 12 paralogs of desulfoglucosinolate sulfotransferase were found in B. rapa, whereas only three were found in Arabidopsis. The expression of those paralogs was not tissue-specific but varied greatly depending on B. rapa tissue types. Expression was also developmentally regulated in some paralogs but not in other paralogs. Most of the regulator genes are present as triple copies. Accordingly, glucosinolate synthesis and regulation in B. rapa appears to be more complex than that of Arabidopsis. With the isolation and further characterization of the endogenous genes, health-beneficial vegetables or desirable animal feed crops could be developed by metabolically engineering the glucosinolate pathway.

The first generation of a BAC-based physical map of Brassica rapa.

BACKGROUND: The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. RESULTS: A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. CONCLUSION: The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.