Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species.

BACKGROUND: Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species. RESULTS: In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum. CONCLUSION: Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus).

BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines.

KEY MESSAGE: Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

Relationship Between Symptom Burden and Self-Management Among Patients with Chronic Heart Failure: A Cross-Sectional Study.

Background: Chronic heart failure (CHF) is a cardiovascular disease that seriously jeopardizes global human health. Studies indicate that good self-management can be effective in controlling disease symptoms. However, there is still insufficient evidence on the association between self-management and symptom burden among CHF patients. This study aimed to observe and assess the correlation of the self-management with the symptom burden and each dimension status in patients with CHF. Methods: This was a cross-sectional study. Data were collected in-hospital using convenience sampling, and 128 patients with CHF were included. A general data questionnaire was used to collect demographic and disease-related data. The Memorial Symptom Assessment Scale-Heart Failure was used to measure patients' symptom burdens. The Heart Failure Self-Management Scale was used to measure the self-management level of patients. The correlation between self-management and symptom burden was analyzed using the Spearman correlation. Results: The total scores for symptom burden and self-management were 1.26 ± 0.49 and 49.97 ± 7.14, respectively. The total score of self-management was negatively correlated with that of symptom burden. The univariate linear regression analysis indicated that age, place of residence, smoking, residence status, New York Heart Association grade of cardiac function, and attitude toward the disease were risk factors for symptom burden. The multiple linear regression analysis indicated that the regression model with symptom burden as a dependent variable included three variables: drug management, symptom management, and attitude toward the disease. Conclusion: Hospitalized patients with CHF had heavy overall symptom burdens, and their self-management levels were moderate to low. There was a negative correlation between the total self-management score and each dimension of symptom burden.

[Anaplastic lymphoma kinase-positive adenocarcinoma of lung: a cytopathologic analysis].

OBJECTIVE: To study the cytomorphologic features of anaplastic lymphoma kinase (ALK)-rearranged pulmonary adenocarcinoma. METHODS: The morphologic features in 153 pulmonary adenocarcinoma cytology specimens encountered during the period from September, 2011 to April, 2015 in Shanghai Cancer Hospital were retrospectively reviewed. Fluorescence in-situ hybridization (FISH) and/or immunohistochemistry (Ventana D5F3) for ALK gene rearrangement were carried out. The samples studied included 34 pleural effusion specimens, 40 endobronchial ultrasound-guided transbronchial needle aspirates (EBUS-TBNA) and 79 fine needle aspirates of palpable masses on body surface. RESULTS: Thirty-nine cases (25.5%) of ALK-rearranged samples were identified by FISH and/or immunohistochemistry, including 3 cases diagnosed by FISH and 36 cases by both technologies. The median age of the ALK-positive group was 50 years, significantly younger than that of the ALK-negative group (60 years old, P = 0.002). Only 4 of the ALK-positive patients were smokers, which was significantly less than that of the ALK-negative group (P < 0.01). In ALK-positive group, 3 cases showed cribriform pattern with prominent nucleoli, 3 cases showed cribriform pattern with mucin-rich cells and 8 cases showed extracellular mucus with mucin-rich cells. The above cytomorphologic patterns were significantly less common in ALK-negative tumors (P < 0.01). CONCLUSIONS: ALK-rearranged lung adenocarcinoma is associated with certain distinctive morphologic patterns, including cribriform architecture, presence of prominent nucleoli, mucin-rich cells and extracellular mucus, which can be observed in cytology specimens (including conventional smears and cell block sections). These findings, when combined with clinical features, may give clues to detection of ALK-positive cases.

Accuracy of fine needle aspiration biopsy processed by cytologic smear and cell block techniques for the diagnosis of lacrimal gland tumors: a study of 48 cases.

OBJECTIVE: To study the accuracy of fine needle aspiration biopsy (FNAB) processed by smear cytology and cell block (CB) techniques for the diagnosis of lacrimal gland tumors (LGTs). STUDY DESIGN: In a prospective study, we enrolled 48 consecutive patients with LGTs. Immediately after excision of LGTs, the tissues were underwent FNAB with 23-gauge needles. The FNAB samples were processed to produce cytologic smears and CB from which slides were cut for immunohistochemical staining. The remainders were submitted for routine histopathologic processing. The diagnostic value of FNAB was assessed by comparing the FNAB diagnoses to those made by routine histopathology. RESULTS: Cytopathologic evaluations based on smear cytology and CB with sections stained immunohistochemically can distinguish non-epithelial lesions from epithelial ones in all cases. The diagnostic sensitivities, specificities, and accuracies for distinguishing benign from malignant lesions were: cytologic smears--76%, 68%, and 71%, respectively; CB with immunohistochemical staining--88%, 87%, and 88%, respectively. The accuracy of the tissue diagnosis compared to routine histopathology was less for cytologic smears (58%) than for CB with immunohistochemistry (81%; P < 0.05). CONCLUSIONS: FNAB of LGT processed using a CB technique capable of producing immunohistochemically stained slides results in a greater percentage of accurate tissue diagnoses than do cytologic smears, when compared to routine histopathology.

High sensitivity of touch imprint cytology in young patients with invasive lobular carcinoma of the breast.

Invasive lobular carcinoma (ILC) of the breast is a rare type of breast cancer. Metastatic ILC is difficult to identify in sentinel lymph nodes (SLNs) because of its low-grade cytomorphology and its tendency to resemble lymphocytes. Touch imprint cytology (TIC) is a rapid method for evaluating SLNs intraoperatively. We sought to evaluate this technique in the identification of SLN metastases in ILC. A total of 230 SLNs from 88 patients diagnosed with ILC were examined with TIC, and the results were compared with their histological diagnosis. We first confirmed some typical cytological features of SLN metastases in ILC such as a thick eosinophilic background and hyperplasia of small cell lacking adhesion. Further analysis showed that sensitivity of TIC was 60.5 % on per-node basis and 58.3 % on per-patient basis; specificity of TIC was 100 % on per-node basis and 100 % on per-patient basis. Interestingly, when we divided patients according to their ages, the sensitivity of TIC in patients younger than 50 years old greatly increased to 90.9 % on per-node basis and 85.7 % on per-patient basis, whereas the specificity remained 100 % on both per-node basis and per-patient basis. However, different tumor sizes did not clearly change the sensitivity of TIC compared to the overall sensitivity. Patients with tumor size bigger than 1 cm revealed a TIC sensitivity of 59.4 % on per-node basis and 55.0 % on per-patient basis. These results suggest that TIC can be used as a reliable method of detecting SLN metastasis only in young patients with ILC.

[Value of cytopathology in endobronchial ultrasound-guided transbronchial needle aspiration].

OBJECTIVE: To evaluate the role of cytopathology in endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) for lung tumor diagnosis and staging. METHODS: Two-hundred consecutive cases of lung tumor with EBUS-TBNA performed during the period from April, 2009 to September, 2010 in Shanghai Cancer Hospital were retrospectively reviewed. The cytologic diagnoses were categorized as non-diagnostic, negative, suspicious and malignant. When available, cell block preparation and immunohistochemistry were performed. On the 22 positive cases diagnosed by on-site evaluation, epidermal growth factor receptor (EGFR) mutation study was carried out. RESULTS: In the 200 cases of cytology specimens, 122 cases (69.3%) were diagnosed as malignant, 42 cases (23.9%) as benign and 12 cases (6.8%) as suspicious for malignancy. The non-diagnostic rate was 12.0% (24/200). Amongst the 200 cases studied, 140 cases (70.0%) had histologic correlation available (via core biopsy, mediastinoscopic biopsy or surgical excision). The sensitivity and specificity of EBUS-TBNA cytologic diagnoses were 94.4% and 100%, when using histopathologic findings and clinical follow-up data as gold standard. The cell block preparation and immunohistochemistry were useful in subtyping and diagnosis of extrathoracic malignancy. EGFR mutations were detected in 8 cytology samples (36.4%). CONCLUSIONS: EBUS-TBNA is a sensitive and specific tool for diagnosis and staging of lung cancer. The cytology samples can be used for further ancillary investigations including cell block preparation, immunohistochemistry and molecular studies.

[Initial experience on endobronchial ultrasound-guided transbronchial needle aspiration in the diagnosis and staging of lung cancer].

BACKGROUND AND OBJECTIVE: It has been proven that endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) was a new minimally invasive method in the diagnosis for mediastinal lymph nodes. The aim of this study is to evaluate the diagnostic and staging yield of EBUS-TBNA for lung cancer. METHODS: Seventy-five patients with tumors and enlarged mediastinal lymph nodes found by CT underwent the diagnosis by endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) from April 1, 2009 to Febuary 8, 2010. The sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy of EBUS-TBNA were evaluated. RESULTS: Seventy-five patients with 177 lymph node groups (2.4 groups in average) were studied. Histopathological samples were found in 49.33% patients and in 28.81% groups. Overall sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy of EBUS-TBNA for diagnostic were 98.43%, 100.00%, 100.00%, 91.67% and 98.66%, respectively, in per patient analysis and were 95.10%, 100%, 100.00%, 82.93%, and 96.05%, respectively, in per group analysis, higher than CT examination (P < 0.05) expect for sensitivity (P = 0.435). Staging changed in 19 (26.03%) patients after EBUS-TBNA. CONCLUSION: EBUS-TBNA proved to be a safe procedure with a high yield for the diagnosis of lung cancer.

Basal cytokeratin expression in relation to immunohistochemical and clinical characterization in breast cancer patients with triple negative phenotype.

AIMS AND BACKGROUND: To evaluate the immunohistochemical characterization of CK5/6 and CK17 and whether the expression level of the two markers was correlated with clinical outcome or pathological feature in triple negative (ER-, PR-, HER-2-) patients with breast cancer. METHODS AND STUDY DESIGN: We carried out an immunohistochemical assay for CK5/6 and CK17 markers on formalin-fixed invasive carcinoma samples from 112 patients who were diagnosed between 2000 and 2002. All of them had an immunohistochemical triple negative status and follow-up information available. RESULTS: Of the 112 patients characterized by triple negative immunohistochemical status, 82 (73.2%) were disease free with no relapse or metastasis. In total, CK5/6 and CK17 were both determined positive in 33.9% (38/112) of the 112 tumor samples, and 46.4% (52/112) were regarded as positive for CK5/6 or CK17. The Kaplan-Meier curve showed that positive staining for CK5/6, CK17, or CK which means CK5/6 positive or CK17 positive, was associated with worse disease-free survival (P = 0.020, P = 0.032, P = 0.003), and positive staining for CK5/6 or CK was associated with worse overall survival (P = 0.027, P = 0.015). When we considered 91 patients whose pathological type was invasive ductal carcinoma, we found that there was also an association between CK5/6 or CK17 immunostaining and high grade (P = 0.030). In addition, these two markers were also associated with axillary lymph node status (P = 0.044). The Cox regression multiple-factor analysis showed that pathological stage, grade and expression of CK were the factors affecting both disease-free and overall survival, whereas age and menopausal status were independent factors affecting disease-free and overall survival, respectively. CONCLUSIONS; Positive staining for CK5/6 or CK17 was associated with a worse prognosis, high tumor grade and positive axillary lymph nodes.

[Expression of CK5/6 and CK17 and its correlation with prognosis of triple-negative breast cancer patients].

OBJECTIVE: To investigate the correlation of CK5/6 and CK17 expression with clinical outcome in patients with triple-negative [ER(-), PR(-), Her-2(-)] breast cancer. METHODS: 112 patients with breast cancer treated by surgery between 2000 and 2002 were included in this study. All cases were immunohistochemically proven to be triple-negative. Samples of formalin-fixed and paraffin-embedded surgical specimens were obtained for immunohistological examination for CK5/6 and CK17 expression. The correlation of the gene expression with clinicopathological features and outcome of the patients was analyzed. RESULTS: Of the 112 triple-negative patients, five-year disease-free survival rate was 73.2% (82/112). The positive rate of both CK5/6 and CK17 was 21.4% (24/112), either CK5/6 or CK17 positive was 46.4% (52/112). It was shown by Kaplan-Meier curve that positive CK5/6, CK17 or CKs (CK5/6 or CK17 positive) was correlated with poor five-year disease-free survival (P = 0.020, P = 0.032, P = 0.003); and positive staining of CK5/6 or CKs was correlated with poor five-year overall survival (P = 0.027, P = 0.015). Of the 91 patients with invasive ductal carcinoma, a correlation of CK5/6 or CK17 positive staining with high grade differentiation was observed (P = 0.030), and with axillary lymph node metastasis was also noticed (P = 0.044). Multivariate analysis by Cox regression showed that differentiation grade, pathological stage and expression of CK5/6 were factors affecting both the disease-free-survival and overall-survival, while menopausal status was an independent factor affecting the disease-free-survival. CONCLUSION: Positive expression of CK5/6 or CK17 in patients with triple-negative breast cancer is correlated with poor prognosis, high grade differentiation and axillary lymph node metastasis.