The association between chronic obstructive pulmonary disease and autoimmune diseases: a bidirectional Mendelian randomization study.

Objective: Observational studies have reported that chronic obstructive pulmonary disease (COPD) is often accompanied by autoimmune diseases, but the causal relationships between them remain uncertain. In this Mendelian study, we aimed to investigate the potential causal relationship between COPD and four common autoimmune diseases. Methods: We conducted an analysis of summary data on COPD and autoimmune disease using publicly available genome-wide association studies (GWAS) summary data. We initially employed the inverse- variance weighted method as the primary approach to establish the causal impact of COPD on autoimmune diseases in the sample and conducted additional sensitivity analyses to examine the robustness of the results. Subsequently, we performed reverse Mendelian randomization (MR) analyses for the four autoimmune diseases. Finally, the potential for bidirectional causal relationships was assessed. Results: Our MR analysis revealed no significant causal relationship between COPD and any of the studied autoimmune diseases. However, reverse MR results indicated a significant association between rheumatoid arthritis (RA), osteoarthritis (OA) and the risk of developing COPD, with respective odds ratios (OR) of 377.313 (95% CI, 6.625-21487.932, P = 0.004) for RA and 11.097 (95% CI, 1.583-77.796, P = 0.015) for OA. Sensitivity analyses confirmed the robustness of the results. Conclusion: Our findings support a potential causal relationship between autoimmune diseases and COPD, highlighting the importance of considering comorbidities in clinical management of COPD.

High-Q optical resonances with robustness based on the quasi-guided modes in waveguide moiré gratings.

High-Q resonances, especially those with high spectral tunability and large robustness of the Q factors, are always sought in photonic research for enhanced light-matter interactions. In this work, by rotating the 1D ridge grating on a slab waveguide in both the clockwise and counterclockwise directions by a certain angle θ, we show that the original subwavelength lattice can be converted into waveguide moiré gratings (WMGs), with the period increased to a larger value determined by the value of θ. These period-increasing perturbations will cause the First Brillouin Zone (FBZ) of the 1D grating to shrink, and thus convert the non-radiating guided modes with the dispersion band below the light line into quasi-guided modes (QGMs) above the light line, which can be accessed by free space radiations. We present the numerically calculated dispersion band and the Q-values for the QGMs supported by the WMGs with θ = 60°, and demonstrate that high-Q resonances can be achieved in a wide region of the energy-momentum space with the Q-values exhibiting large robustness over wavevectors. As an example of application, we show that the QGMs in the WMGs can be exploited to produce quite high optical gradient forces at different wavenumbers or wavelengths. Our results show that the QGMs supported by the WMGs work as a new type of high-Q resonances and may find prospective applications in various photonic systems.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin.

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

Characterization of NF-Y gene family and their expression and interaction analysis in Phalaenopsis orchid.

The complex of Nuclear Factor Ys (NF-Ys), a family of heterotrimeric transcription factors composed of three unique subunits (NF-YA, NF-YB, and NF-YC), binds to the CCAAT box of eukaryotic promoters to activate or repress transcription of the downstream genes involved into various biological processes in plants. However, the systematic characterization of NF-Y gene family has not been elucidated in Phalaenopsis. A total of 24 NF-Y subunits (4 NF-YA, 9 NF-YB, and 11 NF-YC subunits) were identified in Phalaenopsis genome, whose exon/intron structures were highly differentiated among the PhNF-Y subunits. The distribution of motifs between coding regions of PhNF-YA and PhNF-YB/C was distinct. Segmental and tandem duplication events among paralogous PhNF-Ys were occurred. Six pairs of orthologous NF-Ys from Phalaenopsis and Arabidopsis and five pairs of orthologous NF-Ys from Phalaenopsis and rice involved in the phylogenetic gene synteny were identified. The various cis-elements being responsive to low-temperature, drought and ABA were distributed in the promoters of PhNF-Ys. qRT-PCR analysis indicated all of PhNF-Ys displayed the spatial specificity of expression in different tissues. Moreover, the expression levels of multiple PhNF-Ys significantly changed responding to low-temperature and ABA treatment. Yeast two hybrid and bimolecular fluorescence complementation assays approved the interaction of PhNF-YA1/3 with PhNF-YB6/PhNF-YC7, respectively, as well as PhNF-YB6 with PhNF-YC7. PhNF-YA1/3, PhNF-YB6, and PhNF-YC7 proteins were all localized in the nucleus. Further, transient overexpression of PhNF-YB6 and PhNF-YC7 promoted PhFT3 and repressed PhSVP expression in Phalaenopsis. These findings will facilitate to explore the role of PhNF-Ys in floral transition in Phalaenopsis orchid.

Investigations on the optical forces from three mainstream optical resonances in all-dielectric nanostructure arrays.

Light can exert radiation pressure on any object it encounters, and the resulting optical force can be used to manipulate particles at the micro- or nanoscale. In this work, we present a detailed comparison through numerical simulations of the optical forces that can be exerted on polystyrene spheres of the same diameter. The spheres are placed within the confined fields of three optical resonances supported by all-dielectric nanostructure arrays, including toroidal dipole (TD), anapoles, and quasi-bound states in continuum (quasi-BIC) resonances. By elaborately designing the geometry of a slotted-disk array, three different resonances can be supported, which are verified by the multipole decomposition analysis of the scattering power spectrum. Our numerical results show that the quasi-BIC resonance can produce a larger optical gradient force, which is about three orders of magnitude higher than those generated from the other two resonances. The large contrast in the optical forces generated with these resonances is attributed to a higher electromagnetic field enhancement provided by the quasi-BIC. These results suggest that the quasi-BIC resonance is preferred when one employs all-dielectric nanostructure arrays for the trapping and manipulation of nanoparticles by optical forces. It is important to use low-power lasers to achieve efficient trapping and avoid any harmful heating effects.

Synthesis and biological evaluation of oleanolic acid derivatives with electrophilic warheads as antitumor agents.

Aim: The oleanolic acid derivatives containing electrophilic warheads were synthesized, and their antitumor activities were investigated. Materials & methods: The cytotoxicity of compounds against tumor cells were determined by the MTT method. The antitumor effects of compounds 27a, Y03 and Y04 were evaluated in vitro through a wound-healing assay, apoptosis and cell circle analysis, and cellular reactive oxide species determination. The levels of related proteins in MCF-7 cells treated with Y03 was determined through Western blot analysis. Results & conclusion: Compounds 27a, Y03 and Y04 displayed high cytotoxicity against breast cancer cells and inhibited cell migration, induced apoptosis, arrest cell circle at G0/G1 and promoted cellular reactive oxide species generation. The antitumor mechanism involved inhibition of Akt/mTOR and induction of ferroptosis.

Systematic review of Kaixinsan in treating depression: Efficacy and pharmacological mechanisms.

Introduction: Kaixinsan (KXS) has been in use as an effective classic formulation of traditional Chinese medicine for depression. However, its active components and action mechanism against depression remain elusive. The purpose of this study was to summarize and evaluate the efficacy and potential pharmacological mechanisms of KXS in antidepressant treatment. Materials and methods: Reports on the use of KXS in the treatment of depression were systematically collected from PubMed, Web of Science, Embase, China National Knowledge Infrastructure, Chongqing VIP, and Wanfang Data from the establishment to July 2022, including those on mood disorders in neurological diseases such as Alzheimer's disease. Meta-analysis was conducted with the Review Manager 5.3 software. Online datasets, traditional Chinese medicine system pharmacological analysis platform, GeneCards, online Mendelian inheritance in man, and DisGeNET were used to investigate the depression-related genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments were performed to construct the 'component-target-pathways' network using Metascape online analyses. Result: Ten studies were included in the analysis. Meta-analysis showed that both low-dose KXS (SMD = 19.66, Z = 7.96, and I 2 = 42%) and high-dose KXS (SMD = 23.84, Z = 8.46, and I 2 = 13%) could increase the sucrose preference in depression models. In addition, 5-hydroxytryptamine (5-HT) (SMD = 10.91, Z = 2.95, and I 2 = 50%) returned to normal level after the treatment at low dose KXS. In network pharmacology, 50 active components and 376 gene targets were screened out. AKT1, GAPDH, ALB, TNF, and TP53 were the core target proteins. GO analysis showed that KXS mainly treats depression in biological processes such as response to drugs, cellular calcium ion homeostasis, and regulation of chemical synaptic signal transmission. KEGG results show that the mechanism of action of KXS in treating depression is through neural activity ligand-receptor interaction, the calcium signaling and CAMP signaling pathways. Discussion: The study reveals the active components and potential molecular mechanism of KXS in the treatment of depression and provides evidence for future basic research.

Identification of microRNA158 from Anthurium andraeanum and Its Function in Cold Stress Tolerance.

Anthurium andraeanum is a tropical flower with high ornamental and economic value. Cold stress is one of the major abiotic stresses affecting the quality and value of A. andraeanum; thus, improving the cold tolerance of this species is an important breeding objective. MicroRNAs (miRNAs) have a critical role in plant abiotic stress responses, but their specific molecular regulatory mechanisms are largely unknown, including those related to the cold stress response in A. andraeanum. Here, we identified and cloned the precursor of miR158 from A. andraeanum (Aa-miR158). Both Aa-miR158 and its target gene (c48247) had higher expression levels in strong leaves than in other tissues or organs. Further study revealed that the transcript level of Aa-miR158 was increased by cold stress. Heterologous overexpression of Aa-miR158 improved cold stress tolerance in Arabidopsis, which was associated with decreases in the malondialdehyde (MDA) concentration and relative electrical conductivity (REC) as well as increases in peroxidase (POD) and catalase (CAT) activity. Moreover, overexpressing Aa-miR158 significantly increased the expression of endogenous genes related to cold stress tolerance and reactive oxygen species (ROS) levels in transgenic Arabidopsis under cold stress. Overall, our results demonstrate that Aa-miR158 is significantly involved in the cold stress response and provide a new strategy for cold tolerance breeding of A. andraeanum.

The clinical relevance of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in chronic obstructive pulmonary disease with lung cancer.

Background: Chronic obstructive pulmonary disease (COPD) coexisting with lung cancer is associated with severe mortality and a worse prognosis. Inflammation plays an important role in common pathogenic pathways and disease progression. However, a few studies have identified the clinical value of the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) in COPD with lung cancer, which are systemic inflammatory response markers in the blood. This study aimed to determine the association of the NLR or PLR with clinical characteristics and whether NLR or PLR can be diagnostic markers for COPD with lung cancer. Methods: Between 2015 and 2021, we conducted a retrospective analysis of 236 COPD patients with lung cancer and 500 patients without lung cancer (control group). Clinical information, blood routine examination, and spirometry results were collected and analyzed. The receiver operating characteristic (ROC) curve was used to identify the best cutoff point of NLR or PLR. Multivariate logistic regression analysis was performed to evaluate the association of NLR or PLR with the diagnosis and prognosis of COPD with lung cancer. Results: Compared to patients in the COPD-only group, patients in the lung cancer group had a higher percentage of current smoking and emphysema, and it was found that NLR or PLR was significantly higher in the lung cancer group. Multivariate analysis showed that age, smoking status, FEV1%pred, emphysema, NLR, and PLR were independent risk factors for lung cancer development in COPD. Furthermore, the high level of NLR or PLR was associated with age over 70 years old, current smoking status, and ineligible surgery treatment. The level of PLR or NLR markedly increased with hypercoagulation status, the severity of airflow limitation, and advanced progression of lung cancer. Additionally, the ROC analysis also revealed that elevated NLR or PLR was an independent predictor of COPD in lung cancer patients, TNM stages IIIB-IV at first diagnosis in lung cancer, and ineligible surgery in lung cancer patients. Conclusion: Increased NLR or PLR values might be an important and easily measurable inflammation biomarker to predict the diagnosis and severity of lung cancer with COPD.

Acute exacerbations of chronic obstructive pulmonary disease in a cohort of Chinese never smokers goes along with decreased risks of recurrent acute exacerbation, emphysema and comorbidity of lung cancer as well as decreased levels of circulating eosinophils and basophils.

Acute exacerbations show a significant impact on disease morbidity and mortality in chronic obstructive pulmonary disease (COPD). In contrast to stable COPD, the association of smoking status with clinical and laboratory characteristics in patients with acute exacerbations of COPD (AECOPD) has not been well studied. In this retrospective study, we compared never smokers and ever smokers on their demographic, clinical, and laboratory characteristics in a Chinese clinical cohort of AECOPD. In this cohort comprising 1,034 consecutive patients with AECOPD, never smokers were older (75 vs 70.5 years, padjusted < 0.001) and had a higher body mass index than smokers (21.1 ± 4.0 vs 20.3 ± 3.4, padjusted = 0.028). Furthermore, never smokers showed a decreased risk of recurrent acute exacerbation (13.0 vs 21.8%, padjusted = 0.029), a lower risk of development of emphysema (77.8 vs 89.1%, padjusted < 0.001), a lower prevalence of the co-morbidity of lung cancer (0.5 vs 6.6%, padjusted < 0.001), lower levels of circulating eosinophils (EO; 0.04 × 109/L vs 0.10 × 109/L, padjusted = 0.007) and basophils (BA; 0.02 × 109/L vs 0.03 × 109/L, padjusted = 0.019), and a higher plasma levels of D-dimer (0.62 µg/ml vs 0.51 µg/ml, padjusted = 0.02). Furthermore, multivariate logistic regression analysis identified several risk factor for the recurrent acute exacerbation, such as smoking [odds ratio (OR) = 1.84, 95% CI: 1.03-3.40, p = 0.044], urban residential area (OR = 1.43, 95% CI: 1.01-2.05, p = 0.045), and the presence of emphysema (OR = 2.31, 95% CI: 1.25-4.69, p = 0.012). In conclusion, this study demonstrates that the smoking status of patients is associated with recurrent acute exacerbations, emphysema, lung cancer, and levels of circulating EO and BA in AECOPD. Identification of cigarette smoking as a risk factor for recurrent acute exacerbation supports behavioral intervention of smoking cessation in the management of patients with AECOPD.

MicroRNA-495 suppresses cell proliferation and invasion of hepatocellular carcinoma by directly targeting insulin-like growth factor receptor-1.

[This retracts the article DOI: 10.3892/etm.2017.5467.].

Effects of nitric oxide on C2C12 cell inflammatory responses and notexin-induced muscle injury / Efectos del óxido nítrico en las respuestas inflamatorias de las células C2C12 y la lesión muscular inducida por notexina

SUMMARY: Skeletal muscle injury is an acute inflammatory condition caused by an inflammatory response. To reduce inflammatory cell infiltration and relieve skeletal muscle injury, efficient treatment is urgently needed. Nitric oxide is a free radical molecule reported to have anti-inflammatory effects. In this study, we showed that NO could inhibit the inflammatory response of C2C12 cells in vitro and protect rat skeletal muscle injury from notexin in vivo. NO synthase inhibitor (L-NG-Nitroarginine Methyl Este?L-NAME) and NO donor (sodium nitroprusside dehydrate ?SNP) were used to explore the vital role of lipopolysaccharides (LPSs) in LPS-stimulated C2C12 myoblasts.The expression of IL-18 and IL-1b was upregulated by L-NAME and downregulated by SNP, as indicated by the ELISA results. NO can reduce ASC, Caspase-1, and NLRP3 mRNA and protein levels. Furthermore, NO was detected in the rat model. The results of immunohistochemical staining showed that the production of DMD decreased. We conducted qRT-PCR and western blotting to detect the expression of Jo-1, Mi-2, TLR2, and TLR4 on day 6 post injury following treatment with L-NAME and SNP. The expression of Jo-1, Mi-2, TLR2, and TLR4 was upregulated by L-NAME and significantly reversed by SNP. NO can alleviate C2C12 cell inflammatory responses and protect rat skeletal muscle injury from notexin.

RESUMEN: La lesión del músculo esquelético es una afección inflamatoria aguda causada por una respuesta inflamatoria. Para reducir la infiltración de células inflamatorias y aliviar la lesión del músculo esquelético es necesario un tratamiento eficaz. El óxido nítrico es una molécula de radicales libres que tiene efectos antiinflamatorios. En este estudio, demostramos que el ON podría inhibir la respuesta inflamatoria de las células C2C12 in vitro y proteger la lesión del músculo esquelético de rata de la notexina in vivo. El inhibidor de ON sintasa (L-NG-nitroarginina metil este, L-NAME) y el donante de ON (nitroprusiato de sodio deshidratado, SNP) se utilizaron para explorar el papel vital de los lipopolisacáridos (LPS) en los mioblastos C2C12 estimulados por LPS. La expresión de IL- 18 e IL-1b fue regulada positivamente por L-NAME y regulada negativamente por SNP, como indican los resultados de ELISA. El ON puede reducir los niveles de proteína y ARNm de ASC, Caspasa-1 y NLRP3. Además, se detectó ON en el modelo de rata. Los resultados de la tinción inmunohistoquímica mostraron que disminuyó la producción de DMD. Realizamos qRT-PCR y transferencia Western para detectar la expresión de Jo-1, Mi-2, TLR2 y TLR4 el día 6 después de la lesión después del tratamiento con L-NAME y SNP. La expresión de Jo-1, Mi-2, TLR2 y TLR4 fue regulada positivamente por L- NAME y significativamente revertida por SNP. El ON puede aliviar las respuestas inflamatorias de las células C2C12 en ratas, y proteger la lesión del músculo esquelético de la notexina.

FT-like paralogs are repressed by an SVP protein during the floral transition in Phalaenopsis orchid.

KEY MESSAGE: An SVP protein, PhSVP, bound to the CArG-boxes in the promoter regions of FT-like paralogs and repressed their expression, thus affecting the floral transition in Phalaenopsis orchid. Phalaenopsis is an important ornamental flower native to tropical rain forests. It usually reaches vegetative maturity after 4-5 leaves and, after a juvenile stage, forms a flower spike (inflorescence) from the axillary buds. The PEBP gene family encodes a phosphatidyl-ethanolamine-binding protein (PEBP) domain involved in regulating flowering and other aspects of plant development. Here, we identified eight PEBP family genes in Phalaenopsis and detected the expression patterns of seven of them in various organs. Among them, PhFT1 (Phalaenopsis hybrid FLOWERING LOCUS T1), PhFT3, PhFT5, and PhMFT (Phalaenopsis hybrid MOTHER OF FT AND TFL1) promoted flowering in transgenic Arabidopsis, while PhFT6 inhibited flowering. PhSVP (Phalaenopsis hybrid SHORT VEGETATIVE PHASE), an SVP protein that repressed flowering in Arabidopsis, bound to the CArG-boxes in the promoter regions of PhFT3, PhFT6, and PhMFT in a yeast one-hybrid assay. Additionally, dual-luciferase and transient expression assays showed that PhSVP significantly inhibits the expression of both PhFT3 and PhFT6. Together, our work provides a comprehensive understanding of the PhFT-like genes that can promote or repress flowering, and it suggests strategies for regulating the floral transition in Phalaenopsis that exploit the evolutionary versatility of PhFTs to respond to various signals stimuli.

Formation of Phases and Microstructures in Al-8Si Alloys with Different Mg Content.

Mg-containing high-silicon aluminum alloy is a heat-treatable aluminum alloy that is now widely used in the aerospace and automotive industries because of its high specific strength, high wear resistance and corrosion resistance, low thermal expansion coefficient, and low cost. More attention has been paid to optimizing the microstructure to increase the performance of this type of aluminum alloy. In the present work, the solidification processes of Mg-free and Mg-containing (0.33-1.32%) Al-8Si alloys were analyzed by the experimental results combined with the thermodynamic calculation. The results showed that α-Al, Si, and Al5FeSi were in the Mg-free Al-8Si alloy ingots, while the Al5FeSi phases in alloys with Mg additions were transformed into π phases (Al8Mg3FeSi6) by the reaction L+Al5FeSi→α-Al+Si+Al8Mg3FeSi6. There was a binary eutectic reaction of L→α-Al+Al5FeSi when the Mg content exceeded 0.51% and the Fe content was higher than 0.17%. With the increase of Mg content, the volume of Mg2Si was gradually increased while the divorced eutectic phenomenon of the quaternary eutectic structure (α-Al+Si+Mg2Si+Al8Mg3FeSi6) was weakened and the eutectic structure was significantly refined.

LncRNA CASC9 promotes proliferation, migration and inhibits apoptosis of hepatocellular carcinoma cells by down-regulating miR-424-5p.

INTRODUCTION AND OBJECTIVES: CASC9 and miR-424-5p are closely related with hepatocellular carcinoma (HCC) progression. This study aimed to evaluate the effect of CASC9 involved with miR-424-5p on the development of HCC. MATERIALS AND METHODS: qRT-PCR was performed to determine the mRNA expressions of CASC9 and miR-424-5p in HCC tissues/cells and adjacent normal tissues/human hepatic epithelial cells, and to analyze the relationship of CASC9 with the clinico-pathological characteristics and prognosis of HCC patients. Then, cell proliferation was measured by CCK-8 and1 clone formation assays. Apoptosis of HCC cells was measured by flow cytometry. Besides, cell migration and invasion were determined by scratch wound-healing and Transwell assays, respectively. DIANA-LncBase V2 and dual luciferase reporter gene assay were used to verify the targeted relationship between CASC9 and miR-424-5p. Bcl-2, Bax and cleaved caspase-3 expressions were detected by Western blot. RESULTS: Higher expression of CASC9 was observed in HCC tissues/ cells than in adjacent normal tissues/ human hepatic epithelial cells, and was closely linked to poor prognosis of HCC, tumor size, TNM stage, differentiation degree, lymph node metastasis and alpha-fetoprotein (AFP). Down-regulation of CASC9 decreased the proliferation, invasion and migration of HCC cells while enhancing apoptosis. Besides, CASC9 was negatively correlated with miR-424-5p. MiR-424-5p inhibitor enhanced cell proliferation, invasion and migration while decreasing apoptosis. Interestingly, siRNA-CASC9 partially offset the effects of miR-424-5p inhibitor on HCC cells. CONCLUSION: CASC9 promoted proliferation, invasion and migration and inhibited apoptosis in HCC cells by inhibiting miR-424-5p.

Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames.

The outbreak of COVID-19 has brought great threat to human health. Its causative agent is a severe acute respiratory syndrome-related coronavirus which has been officially named SARS-CoV-2. Here we report the discovery of extremely low CG abundance in its open reading frames. We found that CG reduction in SARS-CoV-2 is achieved mainly through mutating C/G into A/T, and CG is the best target for mutation. Meanwhile, 5'-untranslated region of SARS-CoV-2 has high CG content and is capable of forming an internal ribosome entry site (IRES) to recruit host ribosome for translating its RNA. These features allow SARS-CoV-2 to reproduce efficiently in host cells, because less energy is consumed in disrupting the stem-loops formed by its genomic RNA. Notably, genomes of cellular organisms also have very low CG abundance, suggesting that mutating C/G into A/T occurs universally in all life forms. Moreover, CG is the dinucleotide related to CpG island, mutational hotspot and single nucleotide polymorphism in cellular organisms. The relationship between these features is worthy of further investigations.

The expression characteristics of methyl jasmonate biosynthesis-related genes in Cymbidium faberi and influence of heterologous expression of CfJMT in Petunia hybrida.

Cymbidium faberi Rolfe (Orchidaceae) is an herbaceous plant native to China, where it has a long history of cultivation owing to its beautiful flower pattern and floral fragrance. Previously, we conducted a transcriptome analysis of the flower and vegetative buds to elucidate the mechanisms of flower development in C. faberi. In the present study, we found nine secondary metabolic pathways through the KEGG pathway database that were related to the biosynthesis of methyl jasmonate (MeJA) and other volatile organic compounds. qRT-PCR was performed to analyze the expression levels of four key genes in the MeJA pathway. Among these, CfJMT (jasmonic acid carboxyl methyltransferase) had higher transcript levels in sepals, petals and labella than in other tissues. CfJMT was cloned from the petals of full-bloom flowers of C. faberi. The predicted CfJMT protein sequence contains conserved jasmonic acid methyl transferase-7 domains, indicating that it belongs to the SABATH protein family. The CfJMT coding sequence driven by the CaMV35S promoter was successfully transformed into Petunia hybrida through an Agrobacterium-mediated method. Although MeJA could not be detected in either wild-type or transgenic petunia plants, the leaves of the transgenic plants were smaller than those of wild-type plants and pollen development was abnormal. These results indicate that heterologous expression of CfJMT may change the levels of endogenous jasmonic acid and other hormones, but that the content of MeJA is not increased significantly by transformation with CfJMT alone. Thus, other related genes and regulation factors may play important roles in this process.

Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences.

Introns are well known for their high variation not only in length but also in base sequence. The evolution of intron sequences has aroused broad interest in the past decades. However, very little is known about the evolutionary pattern of introns due to the lack of efficient analytical method. In this study, we designed 2 evolutionary models, that is, mutation-and-deletion (MD) and mutation-and-insertion (MI), to simulate intron evolution using randomly generated and mutated bases by referencing to the phylogenetic tree constructed using 14 chordate introns from TF4 (transcription factor-like protein 4) gene. A comparison of attributes between model-generated sequences and chordate introns showed that the MD model with proper parameter settings could generate sequences that have attributes matchable to chordate introns, whereas the MI model with any parameter settings failed in doing so. These data suggest that the surveyed chordate introns have evolved from a long ancestral sequence through gradual reduction in length. The established methodology provides an effective measure to study the evolutionary pattern of intron sequences from organisms of various taxonomic groups. (C++ scripts of MD and MI models are available upon request.).

Phylogenetic analysis of achaete-scute complex genes in metazoans.

Achaete-scute complex (ASC) genes play essential roles in regulating neurogenesis of metazoans. Various metazoan species have greatly different numbers of genes in ASCa, ASCb and ASCc families. To explore evolutionary mechanisms of metazoan ASC genes, Blast (basic local alignment search tool) searches and phylogenetic analyses were conducted to identify ASC genes in metazoan species and to infer phylogenetic relationship between various ASC genes. As a result, 2784 ASC genes were identified in 804 metazoan species. The phylogenetic tree constructed using 1237 unique bHLH motifs shows that metazoan ASCa, ASCb and ASCc families contain six (a1-a6), five (b1-b5) and three (c1-c3) bHLH genes, respectively. Further phylogenetic analyses suggest that ASC genes in metazoans are derived from a primitive c gene, those in insects are derived from c2 gene, and those in chordates are derived from a2 and a3 genes. Data of gene linkage demonstrate that insect a6 is derived from a4 but not from a5, and chordate a2 is ancestral to b5 only, whilst a3 is ancestral to both b3 and b5. It is concluded that current ASC gene families in metazoans were established through a series of sub- and/or neo-functionalization to duplicated ancestral ASC gene(s). These results provide good references for exploring evolutionary mechanisms of other bHLH genes in metazoans. Besides, gene subtyping is considered as an efficient method for evolutionary studies on closely related homologous genes.