The complete chloroplast genome and phylogenetic analysis of Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988

Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988, a member of the Leguminosae family, Cercidoideae subfamily, and Bauhinia genus, has a rich history of traditional usage in Chinese medicine. Renowned for its analgesic properties, it is commonly employed for managing inflammation and pain. This study aimed to sequence the complete chloroplast genome of B. glauca subsp. hupehana using Illumina paired-end sequencing data. The chloroplast genome spans 156,967 bp and consists of four main regions: the large single-copy (LSC) region (89,185 bp), the small single-copy (SSC) region (19,146 bp), and a pair of inverted repeats (IRs) (24,318 bp). The overall GC content of the chloroplast genome is 36.19%, with specific values of 33.99%, 29.79%, and 42.76% for the LSC, SSC, and IR regions, respectively. A total of 128 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that B. glauca subsp. hupehana is closely related to Bauhinia racemose, indicating a sister taxon relationship between the two species. This study significantly contributes to the chloroplast genomic resource for Bauhinia, laying the groundwork for future phylogenetic investigations within the genus.

Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae)

The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.

Distribution Pattern of N6-Methyladenine DNA Modification in the Seashore Paspalum (Paspalum vaginatum) Genome

N6-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, in some of them, it plays important role in the regulation process of stress-resistance response. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in halophyte Seashore paspalum (Paspalum vaginatum) remain largely unknown. Here, we examined the 6mA landscape in the P. vaginatum genome by adopting single molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the P. vaginatum genome. We demonstrated distinct 6mA methylation levels and 6mA distribution patterns in different types of transcription genes, which hinted at different epigenetic rules. Furthermore, the moderate 6mA density genes in P. vaginatum functionally correlated with stress resistance, which also maintained a higher transcriptional level. On the other hand, a specific 6mA distribution pattern in the gene body and near TSS was observed in gene groups with higher RNA expression, which maybe implied some kind of regularity between 6mA site distribution and the protein coding genes transcription was possible. Our study provides new insights into the association between 6mA methylation and gene expression, which may also contribute to key agronomic traits in P. vaginatum.

Candidate genes association study to identify allele-specific SNP marker of ω-3 fatty acid in Brassica napus

Due to the rapid decline in oceanic fish stock, ω-3 fatty acid (C18:3) has attracted serious attention and, hence, the identification of genotypes with high ω-3 content has become the main objective of Brassica napus (rapeseed) breeding. A candidate genes association study permitted us to delineate a genomic region linked to ω-3 content, offering a detailed understanding of the complex genetic mechanism of fatty acid biosynthesis in B. napus. Herein, the candidate genes association study, conducted on 324 genetically diverse rapeseed accessions, detected 114 single nucleotide polymorphisms (SNPs) associated with ω-3 fatty acid. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae. These associated loci were selected based on their contribution to a high C18:3 ratio, and the selected candidate loci were validated using allele-specific SNPs markers in an inbred population through polymerase chain reaction (PCR). These findings may contribute to improving the fatty acid composition by marker-based breeding and will facilitate the development of rapeseed varieties with high ω-3 content.

BnaMPK6 is a determinant of quantitative disease resistance against Sclerotinia sclerotiorum in oilseed rape

Sclerotinia sclerotiorum causes a devastating disease in oilseed rape (Brassica napus), resulting in major economic losses. Resistance response of B. napus against S. sclerotiorum exhibits a typical quantitative disease resistance (QDR) characteristic, but the molecular determinants of this QDR are largely unknown. In this study, we isolated a B. napus mitogen-activated protein kinase gene, BnaMPK6, and found that BnaMPK6 expression is highly responsive to infection by S. sclerotiorum and treatment with salicylic acid (SA) or jasmonic acid (JA). Moreover, overexpression (OE) of BnaMPK6 significantly enhances resistance to S. sclerotiorum, whereas RNAi in BnaMPK6 significantly reduces this resistance. These results showed that BnaMPK6 plays an important role in defense to S. sclerotiorum. Furthermore, expression of defense genes associated with SA-, JA- and ethylene (ET)-mediated signaling was investigated in BnaMPK6-RNAi, WT and BnaMPK6-OE plants after S. sclerotiorum infection, and consequently, it was indicated that the activation of ET signaling by BnaMPK6 may play a role in the defense. Further, four BnaMPK6-encoding homologous loci were mapped in the B. napus genome. Using the allele analysis and expression analysis on the four loci, we demonstrated that the locus BnaA03.MPK6 makes an important contribution to QDR against S. sclerotiorum. Our data indicated that BnaMPK6 is a previously unknown determinant of QDR against S. sclerotiorum in B. napus.

Candidate genes-association study to identify loci related to oleic acid in Brassica napus using SNP markers and their heterologous expression in yeast

Brassica napus (rapeseed) serves as a main source of edible oil, and the oil's quality is mainly determined by the relative proportions of fatty acids. A high oleic acid concentration in B. napus oil increases its shelf life and oxidative stability. Therefore, attaining a high oleic acid concentration is necessary to enhance the nutritional quality of rapeseed oil. Here, an association study of candidate genes was conducted using a population of 324 genetically diverse rapeseed accessions, and several loci related to oleic acid content were identified. Furthermore, these loci were functionally characterized in Saccharomyces cerevisiae to assess their functions, and the promising candidate loci were validated using single nucleotide polymorphic markers in an independent inbred population. The results increased our understanding of fatty acid metabolism in B. napus. Moreover, these findings may assist in marker-based breeding efforts to improve the fatty acid composition and quality of B. napus oil.

BnaMPK3 Is a Key Regulator of Defense Responses to the Devastating Plant Pathogen Sclerotinia sclerotiorum in Oilseed Rape

The disease caused by Sclerotinia sclerotiorum has traditionally been difficult to control, resulting in tremendous economic losses in oilseed rape (Brassica napus). Identification of important genes in the defense responses is critical for molecular breeding, an important strategy for controlling the disease. Here, we report that a B. napus mitogen-activated protein kinase gene, BnaMPK3, plays an important role in the defense against S. sclerotiorum in oilseed rape. BnaMPK3 is highly expressed in the stems, flowers and leaves, and its product is localized in the nucleus. Furthermore, BnaMPK3 is highly responsive to infection by S. sclerotiorum and treatment with jasmonic acid (JA) or the biosynthesis precursor of ethylene (ET), but not to treatment with salicylic acid (SA) or abscisic acid. Moreover, overexpression (OE) of BnaMPK3 in B. napus and Nicotiana benthamiana results in significantly enhanced resistance to S. sclerotiorum, whereas resistance is diminished in RNAi transgenic plants. After S. sclerotiorum infection, defense responses associated with ET, JA, and SA signaling are intensified in the BnaMPK3-OE plants but weakened in the BnaMPK3-RNAi plants when compared to those in the wild type plants; by contrast the level of both H₂O₂ accumulation and cell death exhibits a reverse pattern. The candidate gene association analyses show that the BnaMPK3-encoding BnaA06g18440D locus is a cause of variation in the resistance to S. sclerotiorum in natural B. napus population. These results suggest that BnaMPK3 is a key regulator of multiple defense responses to S. sclerotiorum, which may guide the resistance improvement of oilseed rape and related economic crops.

Two-phase quasi-equilibrium in β-type Ti-based bulk metallic glass composites

The microstructural evolution of cast Ti/Zr-based bulk metallic glass composites (BMGCs) containing β-Ti still remains ambiguous. This is why to date the strategies and alloys suitable for producing such BMGCs with precisely controllable volume fractions and crystallite sizes are still rather limited. In this work, a Ti-based BMGC containing β-Ti was developed in the Ti-Zr-Cu-Co-Be system. The glassy matrix of this BMGC possesses an exceptional glass-forming ability and as a consequence, the volume fractions as well as the composition of the β-Ti dendrites remain constant over a wide range of cooling rates. This finding can be explained in terms of a two-phase quasi-equilibrium between the supercooled liquid and β-Ti, which the system attains on cooling. The two-phase quasi-equilibrium allows predicting the crystalline and glassy volume fractions by means of the lever rule and we succeeded in reproducing these values by slight variations in the alloy composition at a fixed cooling rate. The two-phase quasi-equilibrium could be of critical importance for understanding and designing the microstructures of BMGCs containing the β-phase. Its implications on the nucleation and growth of the crystalline phase are elaborated.

A paired case-control comparison of ziprasidone on visual sustained attention and visual selective attention in patients with paranoid schizophrenia

OBJECTIVE

Cognitive impairment is one of the main targets of the treatment to schizophrenia.The atypical antipsychotic was proved to improve the cognition function of the patients. There were a few of clinical trials to detect the effect of medicine treatment on attention function. But the respective changes of sustained and selective attention in the patients with treatment of ziprasidone were rarely investigated. This present study was to explore the effect of ziprasidone on visual sustained and selective attention in schizophrenia.

PATIENTS AND METHODS

There were 81 patients who were treated with ziprasidone and matched with 81 healthy controls in this open-label trial. The functions were evaluated by Continuous Performance Test (CPT) and Color Word Test (CWT) at baseline and eight weeks later. Between two groups the functions were compared at the two time points, and in patients group those were compared prior to and post treatment.

RESULTS

As compared with healthy controls, the functions of the patients were worse. But after 8 weeks treatment of ziprasidone the functions improved in some degree, which were indicated by the change of CPT and CWT indexes. Furthermore, those of patients post treatment were better than prior to treatment.

CONCLUSIONS

Patients with paranoid schizophrenia have visual sustained and selective attention deficits. The deficits can be improved partly with ziprasidone treatment.

Impact of secondary cytoreductive surgery on survival of patients with advanced epithelial ovarian cancer

AIMS

To investigate the impact on survival of secondary cytoreduction for advanced epithelial ovarian cancer and variables influencing redebulking surgical outcome.

METHODS

Between 1986 and 1997, 106 patients who received secondary cytoreductive surgery and consequent second-line chemotherapy for stages III and IV epithelial ovarian cancer were retrospectively reviewed. The optimal residual disease cut-off was 1.0 cm. The Cox proportional regression model and logistic stepwise regression were used in statistical processing of the data.

RESULTS

The median age of the patients was 50 years (range, 26-77 years). Optimal secondary cytoreduction was achieved in 46 of 106 patients (43.4%). There was a significant difference in survival between patients who were optimally cytoreduced compared to those suboptimaly cytoreduced, with an estimated median survival in the optimal group of 20 months vs 8 months in the suboptimal group ((2)=42.03, P=0.0000). When factorized, patients had significant survival benefit from optimal secondary cytoreduction for recurrent disease and interval cytoreduction. Survival was adversely influenced by progression-free interval < or =12 months (P=0.0078), residual disease >1 cm (P=0.0001) and presence of refractory ascites (P=0.0001). The probability of successful redebulking surgery was affected by presence of refractory ascites (P=0.0023) in all 106 patients and by the ascites (P=0.0072) and residual disease at initial operation in recurrent disease (P=0.0096).

CONCLUSION

Secondary surgical cytoreduction surgery significantly lengthened survival for patients with recurrent epithelial ovarian cancer or those receiving interval cytoreduction. Patients with refractory ascites, however, were not suitable for aggressive secondary surgery, and redebulking surgery for those with residual disease of >1.0 cm after primary operation should be considered prudently in recurrent disease.

Effect of cytoreductive surgery on survival of patients with recurrent epithelial ovarian cancer

BACKGROUND AND OBJECTIVES

The value of secondary cytoreductive surgery is still controversial, especially in patients with recurrent epithelial ovarian cancer. In this retrospective study, we investigated the effect on survival of secondary cytoreduction for recurrent disease and variables influencing redebulking surgical outcome.

METHODS

Between 1986 and 1997, 60 patients who received primary cytoreductive surgery and platinum-based chemotherapy for stage III and IV epithelial ovarian cancer experienced disease recurrence at least 6 months after completion of primary therapy, and secondary surgical cytoreduction was performed. The optimal residual disease cutoff was 1.0 cm. The Cox proportional regression model and Logistic stepwise regression were used in statistical processing of the data.

RESULTS

The median progression-free interval between the two operations was 13 months (range, 6-56 months). Optimal secondary cytoreduction was achieved in 23 patients (38.33%). There was a significant difference in survival between patients who were optimally cytoreduced compared to those suboptimally cytoreduced, with an estimated median survival in the optimal group of 19 months vs. 8 months in the suboptimal group (chi(2) = 22.04, P = 0.0000). Prognosis of survival for individuals with progression-free interval >12 months was better than that of those with the interval </=12 months (chi(2) = 5.22, P = 0.0224). Patients with ascites at disease recurrence suffered a pessimistic outcome, with an estimated median survival of 6 vs. 13 months in those without ascites (chi(2) = 13.99, P = 0.0002). Multivariate analysis strongly suggested that residual disease after second operation, ascites at disease recurrence, and progression-free interval were independent prognostic factors of survival. Logistic stepwise regression revealed that recurrent ascites (P = 0.0072, relative risk = 20.36) and residual disease after the second operation (P = 0.0096, relative risk = 5.16) were important determinants of secondary surgical outcome.

CONCLUSIONS

Secondary cytoreductive surgery significantly lengthened survival for patients with recurrent epithelial ovarian cancer. Patients with ascites at disease recurrence, however, were not suitable for aggressive secondary surgery, and redebulking surgery for those with residual disease of >1.0 cm after primary operation should be considered prudently.

Epithelial ovarian cancer presenting initially with extraabdominal or intrahepatic metastases: a preliminary report of 25 cases and literature review

The purpose of this study was to investigate the clinical features of patients with epithelial ovarian cancer (EOC) that are initially categorized as extraabdominal adenocarcinoma of unknown primary. Twenty-five patients with EOC, who were treated in the Cancer Hospital of Shanghai Medical University from January 1986 to December 1997, and manifesting as extraperitoneal or liver parenchyma metastases at the time of presentation without detectable ovarian tumors, were retrospectively studied. Sixteen patients (64%) were optimally surgical debulked. When compared with 52 other women with stage IV EOC, 20 patients who initially sought treatment for extraabdominal metastases experienced a better prognosis, with an estimated median survival of 24 months versus 10 months (p = 0.0427). The median survival was 30 months in patients with pleural effusion or supraclavicular lymph node metastases versus 19 months in those with spread to other sites (p = 0.0264). The prognosis of such cases, mainly for those with supraclavicular lymphadenopathy or malignant pleural effusion, is better than that for other stage IV EOC patients, probably because most of the patients who initially had distant metastases were generally in condition that permitted aggressive surgery or multicycle chemotherapy.

Cytoreductive surgery for stage IV epithelial ovarian cancer

We tried to determine the role of cytoreductive surgery for stage IV epithelial ovarian cancer and in what conditions this surgical procedure could carry the best benefits. From January 1986 to December 1997, seventy-one of 73 patients with stage IV epithelial ovarian cancer who were treated in Cancer Hospital of Shanghai Medical University were retrospectively reviewed. Clinical information including age, grade, histology, presence of ascites, size of residual disease, site of extra-abdominal metastasis, whether initially presenting as metastatic disease or not, neo-adjuvant chemotherapy, platinum-based chemotherapy and second-line chemotherapy was obtained. Survival was calculated by life-table and survival curves were computed using the Kaplan-Meier method with differences in survival estimated by log-rank test. Independent prognostic factors were identified by Cox's proportional hazards regression model. The median age of the patients' population was 54 years (range 22-82), median follow-up time was 12 months (range 3 to 130) and estimated 5-year survival rate 6.1%. Thirty out of 71 (42.3%) patients were successfully debulked (< or = 1 cm) at the time of initial surgery. There was a significant difference in five-year survival rate between patients optimally (14.1%) vs suboptimally (0%) cytoreduced, with an estimated median survival in the optimal group of 23 months vs 9 months in the suboptimal group (P=0.0001, long-rank test). When the variables were factorized, only in patients with malignant pleural effusion or positive supraclavicular lymph nodes, optimal cytoreduction could get the greatest benefits. Multivariate analysis revealed that the size of residual disease and ascites were independent factors of survival. However, only ascites was the prognostic factor of progression-free survival. Optimal cytoreductive surgery is an important determinant of survival in women with stage IV epithelial ovarian cancer, mainly in those with malignant pleural effusion or positive supraclavicular lymph node pathology.

Self-reported depressive symptoms among Chinese adolescents

Previous reports on the prevalence and features of depression among adolescents have been inconsistent. The purpose of the current study was to estimate the prevalence of depression among Chinese adolescents with a standardized instrument. A total of 2462 students, aged 13-22, were sampled from the Shandong province of China. The Zung Self-Rating Depression Scale (SDS) was administered to the subjects in their classrooms. It was shown that the mean SDS score was 44.8 (SD 9.9) and it decreased significantly from the age of 18 upward (F = 31.73, df = 9, P < 0.01). No significant difference was found between males and females (t = 0.70, P > 0.05). Taking 55 as a cut-off score, the prevalence rate of depression was 16.9% (95% CI = 15.4-18.4%). Logistic regression showed that increasing age appeared to decrease the risk for depression. Most of the individual items differed between ages, except for weight loss and constipation. Principal components factor analysis revealed that the characteristics of adolescent depression were depressive/anxious mood, psychomotor retardation, loss of self-esteem, somatic symptoms and decreased appetite and libido. Although the study was based on a large sample using an established instrument, the sample was not from a general adolescent population and case ascertainment was not by clinical diagnosis.

The trypsin-catalyzed activation of glutamate dehydrogenase purified from eel liver

Eel liver glutamate dehydrogenase (GDH) [EC 1.4.1.3] was eightfold activated by trypsin and the molecular weight of the subunit of the native GDH decreased from 54,000 to 50,000. The C-terminal amino acid of both subunits was Thr. One peptide was released after proteolysis of the native GDH by trypsin and purified by anhydrotrypsin agarose and reversed-phase HPLC. The isolated peptide consisted of 39 amino acids and its amino acid sequence was as follows: H2NS-E-A-V-E-K-E-D-D-P-N-F-F-K-M-V-E-G-F-F-D-K-G-A-A-I- V-E-N-K-L-V-E-E-D-L-K-T-R-COOH. The peptide contained the N-terminal of the native GDH and its molecular weight was calculated to be 4,413. We concluded that the trypsin-catalyzed activation was caused by release of this peptide from the native GDH. p-Chloromercuribenzoic acid inhibited the activity of the trypsin-treated GDH, but stimulated that of the native GDH. The response of trypsin-treated GDH to ADP and GTP was decreased compared with that of the native GDH.