Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota

Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500 mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-κB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.

Engineering of human tryptophan hydroxylase 2 for efficient synthesis of 5-hydroxytryptophan

L-Tryptophan hydroxylation catalyzed by tryptophan hydroxylase (TPH) presents a promising method for synthesizing 5-hydroxytryptophan (5-HTP), yet the limited activity of wild-type human TPH2 restricts its application. A high-activity mutant, MT10 (H318E/H323E), was developed through semi-rational active site saturation testing (CAST) of wild-type TPH2, exhibiting a 2.85-fold increase in kcat/Km over the wild type, thus enhancing catalytic efficiency. Two biotransformation systems were developed, including an in vitro one-pot system and a Whole-Cell Catalysis System (WCCS). In the WCCS, MT10 achieved a conversion rate of only 31.5 % within 32 h. In the one-pot reaction, MT10 converted 50 mM L-tryptophan to 44.5 mM 5-HTP within 8 h, achieving an 89 % conversion rate, outperforming the M1 (NΔ143/CΔ26) variant. Molecular dynamics simulations indicated enhanced interactions of MT10 with the substrate, suggesting improved binding affinity and system stability. This study offers an effective approach for the efficient production of 5-HTP.

[One case of severe exogenous lipoid pneumonia complicated with lung abscess caused by diesel inhalation]

Exogenous lipoid pneumonia is an inflammatory response to the lungs caused by inhaled lipid substances, which is prone to secondary bacterial infection, resulting in the formation of local abscesses, which can be life-threatening in severe cases. This paper reports a case of a 55-year-old patient with diesel aspiration, secondary to Klebsiella pneumoniae (ESBL positive) and Candida glabrata infection resulting in lung abscess formation. He was treated with a variety of antibacterial drugs for anti-infection, non-invasive ventilator ventilation, bronchoalveolar lavage, glucocorticoids, phlegm and other medical treatments. Finally, he underwent middle lobectomy for improvement and was discharged from the hospital, and he recovered well with regular follow-up.

Engineering of Shikimate Pathway and Terminal Branch for Efficient Production of L-Tryptophan in Escherichia coli

L-tryptophan (L-trp), produced through bio-manufacturing, is widely used in the pharmaceutical and food industries. Based on the previously developed L-trp-producing strain, this study significantly improved the titer and yield of L-trp, through metabolic engineering of the shikimate pathway and the L-tryptophan branch. First, the rate-limiting steps in the shikimate pathway were investigated and deciphered, revealing that the combined overexpression of the genes aroE and aroD increased L-trp production. Then, L-trp synthesis was further enhanced at the shaking flask level by improving the intracellular availability of L-glutamine (L-gln) and L-serine (L-ser). In addition, the transport system and the competing pathway of L-trp were also modified, indicating that elimination of the gene TnaB contributed to the extracellular accumulation of L-trp. Through optimizing formulas, the robustness and production efficiency of engineered strains were enhanced at the level of the 30 L fermenter. After 42 h of fed-batch fermentation, the resultant strain produced 53.65 g/L of L-trp, with a yield of 0.238 g/g glucose. In this study, the high-efficiency L-trp-producing strains were created in order to establish a basis for further development of more strains for the production of other highly valuable aromatic compounds or their derivatives.

[A case of corrosive digestive tract and lung injury caused by ingestion of pipeline dredging agent]

Ingestion of corrosive substances can severely burn the upper digestive tract leading to bleeding or perforation, and may even be life-threatening. Less commonly, damage to the trachea and bronchi is involved. In this paper, a case of corrosive digestive tract injury and lung injury after oral administration of pipeline dredging agent (the main components are hydroxide, sodium carbonate, sodium hypochlorite, etc.) was analyzed. After active rescue treatment, the patient died of massive hemoptysis. It is suggested that serious complications may occur after ingestion of corrosive substances. Timely diagnosis and reasonable medical management are needed to improve the level of recognition and treatment of such diseases.

[Clinical application of a classification based on crucial curvature of coronal imbalance in degenerative lumbar scoliosis]

Objective: To present efficacy of clinical application of a classification based on crucial curvature of coronal imbalance in degenerative lumbar scoliosis (DLS). Methods: A case series study. Clinical data of 61 cases (8 males, 53 females) who underwent posterior correction surgery for DLS from January 2019 to January 2021 were retrospectively analyzed. The mean age was (71.7±6.2) years (ranged 60-82 years). According to the direction of C₇ plumb line (C₇PL) deviated from central sacral vertical line (CSVL) and orientation of L₄ coronal tilt, the author determined which one was the crucial curve. If C₇PL deviated from CSVL in the same direction as concave side of the thoracolumbar curve and L₄ coronally tilts opposite direction of C₇PL deviates from CSVL, then the crucial curve was thoracolumbar curve (type 1). On the contrary, if C₇PL deviated from CSVL in the same direction as concave side of the lumbosacral curve and L₄ coronally tilts consist with direction of C₇PL deviates from CSVL, then the crucial curve was lumbosacral curve (type 2). According to absolute value of coronal balance distance (|CBD|), each type of patients was divided into two groups, respectively, namely coronal balance (CB) (|CBD|≤3 cm) and coronal imbalance (CIB) (|CBD|>3 cm). Changes of Cobb angles of thoracolumbar curve and lumbosacral curve and CBD were recorded and analyzed. Results: The rate of preoperative CIB was 55.7% (34/61) in all the patients. Of the patients, 23 cases were classified as type 1 and 38 cases as type 2. The rate of preoperative CIB was 34.8% (8/23) in type 1 patients and 68.4% (26/38) in type 2. The rate of postoperative CIB was 27.9% (17/61) in all the patients, with 13.0% (3/23) in type 1 and 36.8% (14/38) in type 2. The |CBD| of CB group in type 1 patients decreased from (2.6±1.4) cm before the operation to (1.5±1.0) cm after (P=0.015); and the correction rate of thoracolumbar curve (68.8%±18.4%) was significantly higher than that of lumbosacral curve (34.5%±23.9%) (P=0.005). The |CBD| of CB group in type 2 patients decreased from (2.6±3.0) cm before the operation to (1.6±1.2) cm after (P=0.027); the correction rate of lumbosacral curve (71.3%±18.6%) was higher than that of thoracolumbar curve (57.3%±21.1%), but the difference was not statistically significant (P=0.546). There was no significant difference in |CBD| of CIB group in type 2 patients before and after the operation (P=0.222); the correction rate of lumbosacral curve (38.3%±14.8%) was significantly lower than that of thoracolumbar curve (53.6%±16.0%) (P=0.001). There was a correlation between the change of CBD (3.8±1.5) cm and the difference in correction rate between thoracolumbar and lumbosacral curve (32.3%±19.6%) in CB group in type 1 patients after surgery (r=0.904, P<0.001). There was a correlation between the change of CBD (1.9±2.2) cm and the difference in correction rate between lumbosacral and thoracolumbar curve (14.0%±26.2%) in CB group in type 2 patients after surgery (r=0.960, P<0.001). Conclusion: Clinical application of a classification based on crucial curvature of coronal imbalance in DLS is satisfactory, and its combination with matching correction can effectively prevent the occurrence of coronal imbalance after spinal correction surgery.

[Willingness of receiving influenza vaccine and its influencing factors among health care workers in Yangtze River Delta region from 2020 to 2021]

Objective: To analyze the willingness of receiving influenza vaccine and its influencing factors among health care workers (HCWs) in Yangtze River Delta region from 2020 to 2021. Methods: Convenient sampling method was adopted. From July 2020 to March 2021, 76 hospitals in Jiangsu, Zhejiang, Anhui and Shanghai provinces were selected according to the hospital level and job position, and a questionnaire survey was conducted on the willingness of receiving influenza vaccination. Logistic regression model was used to analyze the influencing factors of vaccination intention. Results: A total of 1 332 HCWs were investigated, with a ratio of male to female about 1∶3.2, and the length of working years was (15.07±9.75) years. A total of 614 HCWs had received influenza vaccine in 2019, with a vaccination rate of 46.09%. About 63.21% (842/1 332) of HCWs were willing to be vaccinated with influenza vaccine. The results of binary logistic regression analysis showed that the willingness of receiving influenza vaccine among HCWs in primary hospitals was higher than that in secondary hospitals (OR=0.573) and tertiary hospitals (OR=0.357). The willingness of HCWs who had received influenza vaccine in 2019 was higher than that of HCWs who had not received influenza vaccine (OR=0.226) and had unknown history of influenza vaccination (OR=0.228). The willingness of HCWs in departments of prevention, health care and infection was higher than that in departments of pre-examination, outpatient, emergency, pediatrics and respiratory (OR=1.670). Conclusion: The willingness of receiving influenza vaccination among HCWs in Yangtze River Delta region is high, but it is still lower than that in developed countries. It is necessary to strengthen publicity and education to improve the influenza immunization level of HCWs.

Review of DNA repair enzymes in bacteria: With a major focus on AddAB and RecBCD

DNA recombination repair systems are essential for organisms to maintain genomic stability. In recent years, we have improved our understanding of the mechanisms of RecBCD/AddAB family-mediated DNA double-strand break repair. In E. coli, it is RecBCD that plays a central role, and in Firmicute Bacillus subtilis it is the AddAB complex that functions. However, there are open questions about the mechanism of DNA repair in bacteria. For example, how bacteria containing crossover hotspot instigator (Chi) sites regulate the activity of proteins. In addition, we still do not know the exact process by which the RecB nuclease or AddA nuclease structural domains load RecA onto DNA. We also know little about the mechanism of DNA repair in the industrially important production bacterium Corynebacterium glutamicum (C. glutamicum). Therefore, exploring DNA repair mechanisms in bacteria may not only deepen our understanding of the DNA repair process in this species but also guide us in the targeted treatment of diseases associated with recombination defects, such as cancer. In this paper, we firstly review the classical proteins RecBCD and AddAB involved in DNA recombination repair, secondly focus on the novel helical nuclease AdnAB found in the genus Mycobacterium.

[Malignant solitary fibrous tumors: a clinicopathological and molecular genetic analysis]

Objective: To explore the clinicopathological features, immunophenotype and molecular genetic characteristics of malignant solitary fibrous tumor (MSFT). Methods: Seven cases of MSFT were collected from the First Affiliated Hospital of Zhengzhou University from July 2018 to December 2020. Immunohistochemistry, RNA-based NGS and DNA-based NGS were performed. Results Among the 7 patients, there were 5 males and 2 females with a median age of 53 years (37-69 years). Two tumors located at skull base, and one in the tentorium of cerebellum, parietal occipital region, occipital area, chest and buttock respectively. The maximum diameter of the tumor was 2.5-20.0 cm. Microscopically, typical hemangiopericomatoid structures were noted; the tumor was cellular, fusiform or oval, very pleomorphic, with necrosis and high mitotic figures (>4/10 HPF). In some cases, classical solitary fibrous tumor morphology and dedifferentiated region were observed. Immunohistochemically, the tumor was positive for CD34 (6/7), STAT6 (7/7), bcl-2 (7/7), but negative for S-100 (7/7); CKpan or EMA was positive to varying degrees; mutated p53 was noted (3/7); Ki-67 positive index was more than 10%. NAB2-STAT6 gene fusion was typically detected in all the 7 cases. In 4 cases, ZNF415-FGFR1, COPG1-MET, IPO11-LRRC70_ncRNA-PLAG1 and Clorf198-CD274 (PD-L1) gene fusions were also detected. NOTCH1 mutation was found in 7 cases and TP53 mutation in 4 cases. TERT promoter mutations were not detected in all the cases. Conclusions: MSFT is rare and needs to be differentiated from many other spindle cell tumors. Especially when tumors express epithelial markers, they are easily misdiagnosed as sarcomatoid carcinoma and synovial sarcoma, etc. Immunohistochemistry and molecular detection of NAB2-STAT6 gene fusion have important diagnostic values. NOTCH1 and TP53 mutations may be associated with the progression of MSFT. Some patients have FGFR1 gene fusion and MET gene fusion, which may be potential therapeutic targets.

Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs

Intramuscular fat content (IFC) is an essential quantitative trait of meat, affecting multiple meat quality indicators. A certain amount of IFC could not only improve the sensory score of pork but also increase the flavour, tenderness, juiciness and shelf-life. To dissect the genetic determinants of IFC, two methods, including genome-wide efficient mixed-model analysis (GEMMA) and linkage disequilibrium adjusted kinships (LDAKs), were used to carry out genome-wide association studies for IFC in Suhuai pig population. A total of 14 and 18 significant single nucleotide polymorphisms (SNPs) were identified by GEMMA and LDAK, respectively. The results of these two methods were highly consistent and all 14 significant SNPs in GEMMA were detected by LDAK. Seven of the 18 SNPs reached the genome-wide significance level (P < 9.85E-07) while 11 cases reached the suggestive significance level (P < 1.77E-05). These significant SNPs were mainly distributed on Sus scrofa chromosome (SSC) 5, 3, and 7. Moreover, one locus resides in a 2.27 Mb (71.37-73.64 Mb) region on SSC5 harbouring 13 significant SNPs associated with IFC, and the lead SNP (rs81302978) also locates in this region. Linkage disequilibrium (LD) analysis showed that there were four pairs of complete LD (r² = 1) among these 13 SNPs, and the remaining 9 SNPs with incomplete LD (r² ≠ 1) were selected for subsequent analyses of IFC. Association analyses showed that 7 out of 9 SNPs were significantly associated with IFC (P < 0.05) in 330 Suhuai pigs, and the other 2 SNPs tended to reach a significant association level with IFC (P < 0.1). The phenotypic variance explained (PVE) range of these 9 SNPs was 0.92-3.55%. Meanwhile, the lead SNP was also significantly associated (rs81302978) with IFC (P < 0.05) in 378 commercial hybrid pigs (Pietrain × Duroc) × (Landrace × Yorkshire) (PDLY), and the PVE was 1.38%. Besides, two lipid metabolism-relevant candidate genes, the leucine rich repeat kinase 2 (LRRK2) and PDZ domain containing ring finger 4 (PDZRN4) were identified in the 2.27 Mb region on SSC5. In conclusion, our results may provide a set of markers useful for genetic improvement of IFC in pigs and will advance the genome selection process of IFC on pig breeding programmes.

[One case report of pneumoconiosis in porcelain teeth workers]

Porcelain tooth technology is widely used in the treatment of oral diseases, but there are few reports on the possible occupational hazard factors in the process of porcelain tooth production. Porcelain teeth production will produced a large amount of silica dust and metal dust during the grinding process. The technical workers who have been engaged in this work for a long time are very prone to pneumoconiosis due to their poor personal protection awareness. This paper analyzed the clinical data of a pneumoconiosis patient engaged in porcelain tooth making, and analyzed the possible occupational hazard factors in the process of porcelain teeth production, so as to improve the understanding of relevant enterprises, technical workers and medical personnel on the disease and reduce the risk of porcelain teeth production workers suffering from pneumoconiosis.

Integrated microRNA-mRNA analysis reveals the roles of microRNAs in the muscle fat metabolism of Yanbian cattle

Fat deposition is an important economic trait in farm animals. However, it is difficult to genetically improve intramuscular fat deposition via trait-based cattle breeding. The main objectives of this study were to analyze the factors about beef flavor, and to detect functional microRNA (miRNA, miR) associated with intramuscular fat deposition in Yanbian cattle. Longissimus dorsi samples from six steers were separated into high- and low-fat groups (n = 3 each) based on the marbling score, and transcriptomic analysis was performed using miRNA sequencing. A total of 33 miRNAs and 38 genes were found to be differentially expressed in the high- and low-fat groups. Quantitative real-time polymerase chain reaction was performed to validate the sequencing results. Integrated miRNA-mRNA analysis revealed that miRNA-associated target genes were primarily associated with skeletal muscle development. However, some of the miRNAs (miR-424 etc.) and genes (ATF3 etc.) were also associated with fat metabolism. A targeted relationship between miR-22-3p and the WFIKKN2 gene and its involvement in adipocyte differentiation were confirmed experimentally. The study findings may provide potential candidate molecular targets for the selection of cattle with improved meat quality.

Neuropilin-1 is associated with the prognosis of cervical cancer in Henan Chinese population

Objective: Neuropilin-1 has been reported to be a valuable diagnostic biomarker in patients with cervical intraepithelial neoplasia (CIN) and early cervical cancer. The aim of this study was to investigate the association between Neuropilin-1 and the prognosis of cervical cancer in Henan Chinese population.

Methods: Tissues were collected in The Third Affiliated Hospital of Zhengzhou University between 2010 and 2012, determining the level and expression of Neuropilin-1 in different cervical lesions by immunohistochemistry. The cell proliferation assay, wound-healing assays and Transwell assay were performed to explore the ability of proliferation, migration and invasion for Hela and Caski cells after NRP-1 was knocked down by shRNA transfection. Western blotting was performed to investigate the role of NRP-1 in endothelial-to-mesenchymal transition (EndMT). Tumor xenografts model was used to evaluate the effect of NRP-1 on the tumor growth.

Results: The expression of NRP-1 was upregulated in the tumor tissues compared with the CIN and normal tissues (P<0.0001). The overall survival time of the high NRP-1 expression group was significantly shorter than that of the low NRP-1 expression group (P<0.0001); NRP-1-depleted cells had dramatically lower rate of proliferation, migration and invasion compared to control cells (all P<0.05). Depletion of NRP-1 significantly suppressed the growth of CaSki xenograft tumor in nude mice.

Conclusions: The current study demonstrated that NRP-1 expression is significantly correlated with the progression of CC. Notably, high NRP-1 expression is correlated with a poorer survival in patients with CC, and has been shown to be an independent prognostic factor.

Coalescence-Induced Jumping of Two Unequal-Sized Nanodroplets

Coalescence-induced self-propelled jumping of droplets on superhydrophobic surfaces has potential applications for condensation heat transfer enhancement, anti-icing, self-cleaning, antidew, and so forth. However, most of the previous studies focused on two identical droplets which are not commonly encountered in the nature. In this work, coalescence-induced jumping phenomena of two unequal-sized droplets on superhydrophobic surfaces were investigated theoretically and numerically. First, by introducing modified inertial-capillary velocity (u_ic^*) and Ohnesorge number (Oh*) with consideration of radius ratio (r*) of two coalescing droplets, we proposed a generalized inertial-capillary scaling law for the jumping velocity of coalesced droplets, which is expected to be applicable for both two identical droplets and two unequal-sized droplets coalescing on superhydrophobic surfaces. Subsequently, we employed molecular dynamics simulations to investigate the coalescence-induced jumping process of two unequal-sized nanodroplets. Our simulations showed that the dimensionless jumping velocity (v_j/u_ic^*) well follows the generalized inertial-capillary scaling law with v_j/u_ic^* ≈ 0.127 in a specific Oh* range; however, it rapidly reduces and finally vanishes when the radius ratio of large droplet to small droplet is larger than a certain threshold value. Our simulations also revealed that nonjumping of two unequal-sized droplets with a very large radius ratio is due to that the larger droplet swallows the small one, so that the liquid bridge has no chance to impact the solid surface, and hence the "liquid bridge impacting substrate" mechanism fails in this circumstance.

Efficacy and Safety of Chemotherapy Combined with Stereotactic Radiotherapy in the Treatment of Nasopharyngeal Carcinoma

Background

The aim of this study was to investigate the efficacy and safety of chemotherapy (CT) combined with stereotactic radiotherapy (SRT) in the treatment of nasopharyngeal carcinoma (NPC).

Material/Methods

A total of 329 NPC patients without any previous treatment were included in this study between January 2009 and November 2013. These patients were divided into three groups: CT group (n=114), SRT group (n=109), and CT + SRT group (n=106). Contrast-enhanced nasopharyngeal computed tomography (CT)/magnetic resonance (MR) scan was performed on the third month after treatment. Short-term efficacy was evaluated according to the Response Evaluation Criteria in Solid Tumors (RECIST). Toxicity was graded according to the Acute Radiation Morbidity Scoring Criteria (RTOG) and the World Health Organization (WHO) toxicity grading scale. Overall survival (OS), progression free survival (PFS), and incidence rate of acute toxicity (grade ≥3) were calculated after a 24 month follow-up.

Results

Total response rate of all patients was 85.41%. Compared with the CT group and the SRT group, the CT + SRT group showed a substantially improved efficacy in NPC treatment. The incidence rate of the acute toxicity in the CT + SRT group was slightly higher than in the CT group and the SRT group, but the difference was not statistically significant. No treatment-related deaths were observed. The CT + SRT group had the highest two-year OS and PFS, followed by the CT group and the SRT group.

Conclusions

It was shown that NPC patients treated with CT + SRT had better short- and long-term efficacy than those treated with CT or SRT alone.

Determination of eddy current response with magnetic measurements

Accurate mutual inductances between magnetic diagnostics and poloidal field coils are an essential requirement for determining the poloidal flux for plasma equilibrium reconstruction. The mutual inductance calibration of the flux loops and magnetic probes requires time-varying coil currents, which also simultaneously drive eddy currents in electrically conducting structures. The eddy current-induced field appearing in the magnetic measurements can substantially increase the calibration error in the model if the eddy currents are neglected. In this paper, an expression of the magnetic diagnostic response to the coil currents is used to calibrate the mutual inductances, estimate the conductor time constant, and predict the eddy currents response. It is found that the eddy current effects in magnetic signals can be well-explained by the eddy current response determination. A set of experiments using a specially shaped saddle coil diagnostic are conducted to measure the SUNIST-like eddy current response and to examine the accuracy of this method. In shots that include plasmas, this approach can more accurately determine the plasma-related response in the magnetic signals by eliminating the field due to the eddy currents produced by the external field.

[Mutation analysis of GJB2 gene in 1 822 patients with nonsyndromic hearing loss in Zhejiang Province]

Objective:To analyze the genetic characteristics in nonsyndromic hearing impairment (NSHL) patients in Zhejiang province.Method:Peripheral blood samples were obtained from 1822 NSHL patients and 467 normal hearing controls in Zhejiang province. We carried out a systematic mutational screening of GJB2 gene in these subjects by amplifying the coding region of GJB2 gene and sequencing directly.Result:Thirty kinds of mutation were identified, including eleven pathogenic mutations, one hypomorphic allele, sixteen polymorphic mutations and two novel mutations. The c.235delC mutation was the most prevalent pathogenic mutation in this cohort (18.50%), and the rate of allele mutation was 12.16%. The frequency of c.299_300delAT,c.176_191del16,c.512_513insAACG,c.35delG,c.283G>A,c.427C>T,c.35insG,c.439G>A,c.571T>C,c.139G>T mutations were decreased in turn.Conclusion:c.235delC mutation is the hot spot of GJB2 gene mutation in NSHL patients in Zhejiang province and the most common mutational pattern is frame-shift mutation. The discovery of novel mutations enriches the spectrum and frequency of variants in GJB2 gene.

Effects of TiO2 nanoparticles on nutrition metabolism in silkworm fat body

Silkworm (Bombyx mori) is an important economic insect with a fat body that plays a crucial role in the storage and transfer of nutrients. It is also known that TiO₂ nanoparticles (NPs) can improve feed efficiency and promote silk protein synthesis in the silkworm. In this study, we profiled gene expression in the silkworm fat body after TiO₂ NP treatment, validated the major RNA-seq findings, and determined the contents of trehalose and triglyceride, the activity of lipase, and the amount of total proteins. RNA-seq analysis revealed that TiO₂ NP treatment caused significant expression changes in 341 genes (P≤0.01), 138 of which were upregulated while the other 203 were downregulated. The expression levels of two target genes in the insulin signaling pathway and two protein metabolism-related target genes, three lipid metabolism-associated target genes, two carbohydrate metabolism related target genes and expression levels of seven heat shock protein genes were increased, and that of threonine dehydratase gene and fatty acid transport protein gene were decreased. The RNA-seq results of 16 genes were validated by quantitative real-time PCR. The lipase activity, content of trehalose, and amount of total proteins were elevated by 3.86-fold, 1.34-fold, and 1.21-fold, respectively, and the content of triglyceride was decreased by 0.94-fold after TiO₂ NP treatment. These results indicated that TiO₂ NPs activated the insulin signaling pathway, promoted the metabolism of protein, fat, and carbohydrate, and improved nutrition metabolism. Our study provides new support for the understanding of the beneficial effect of TiO₂ NPs on silkworm nutrient metabolism.

Summary: Our study indicates that TiO₂ nanoparticles promote nutrient metabolism in the fat body of silkworms, and provide a reference for studies investigating the biological function of TiO₂ nanoparticles.

Mechanisms of TiO2 NPs-induced phoxim metabolism in silkworm (Bombyx mori) fat body

Silkworm is an important economic insect. Abuse of organophosphorus pesticides in recent years often leads to poisoning of silkworms, which significantly affects sericulture development by reducing silk production. Previous studies have shown that TiO2 NPs can effectively mitigate the damages caused by organophosphorus pesticides in silk glands and nerve tissues. The fat body is an important metabolic detoxification organ of silkworms, but it is unknown whether TiO2 NPs affect pesticide metabolism in fat body. In this study, we characterized the transcription of antioxidant genes and enzyme activity in fat body after TiO2 NPs and phoxim treatments using transcriptome sequencing, real-time PCR, and enzyme activity assay. Transcriptome sequencing detected 10 720, 10 641, 10 403, and 10 489 genes for control group, TiO2 NPs group, phoxim group, and TiO2 NPs+phoxim group, respectively. The TiO2 NPs+phoxim group had 705 genes with significantly differential expression (FDR<0.001), among which the antioxidant genes thioredoxin reductase 1 and glutathione S-transferase omega 3 were significantly upregulated. In phoxim group, the expression levels of superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase delta (GSTd), and thioredoxin peroxidase (TPx) were increased by 1.365 -fold, 1.335 -fold, 1.642 -fold, and 1.765 -fold, respectively. The level changes of SOD, CAT, GSTd, and TPx were validated by real time PCR. The contents of reactive oxygen species (ROS), malondialdehyde (MDA), and hydrogen peroxide (H2O2) were increased by 1.598 -fold, 1.946 -fold, and 1.506 -fold, respectively, indicating that TiO2 NPs treatment can relieve phoxim-induced oxidative stress. To clarify the mechanism of TiO2 NPs's effect, the transcription levels of P450 gene family were measured for the TiO2 NPs+phoxim group; the expression levels of CYP4M5, CYP6AB4, CYP6A8, and CYP9G3 were elevated by 2.784 -fold, 3.047 -fold, 2.254 -fold, and 4.253 -fold, respectively, suggesting that high expression of P450 family genes can enhance the metabolism of phoxim in the fat body. The results of this study indicated that TiO2 NPs treatment promoted the transcriptional expression of the P450 family genes to improve the fat body's ability to metabolize phoxim and reduce phoxim-induced oxidative stress. This may be the main mechanism of TiO2 NPs' mitigation of phoxim-induced damages in the fat body.

Effects of mutations on the structure and function of silkworm type 1 acetylcholinesterase

AChE is the target of organophosphate (OP) and carbamate (CB) pesticides, and mutations in the gene can significantly reduce insects' sensitivity to these pesticides. Bombyx mori is highly sensitive to pesticides. To investigate the effects of mutations on AChE1 structure and function, we used a prokaryotic system to express B.mori wild type AChE1 (wAChE1) and mutant AChE1 (mAChE1) in this study. Active AChE1 proteins were obtained after refolding and purification, and wAChE1 and mAChE1 had similar activities. After incubation with 10(-6)M physostigmine and 10(-3)mg/mL phoxim, the remaining enzyme activity of mAChE1 was 4.42% and 8.86% higher than that of wAChE1's, respectively. Three-dimensional analysis of mutation AChE1 (mAChE1) revealed that the Ser and Ala side chains extended toward the central part of S285 with distances of just 2.80Å and 3.68Å, respectively, which changed the spatial structure of the active center and reduced its sensitivity to pesticides. These results indicated that the mutations altered the 3D structure of AChE1, which may affect the binding of physostigmine and phoxim to the serine residue at the active center, leading to reduced sensitivity. Our study helps understand the relationship between AChE1 mutations and pesticide resistance and provides a new direction for the cultivation of new pesticide-resistant varieties of B.mori.

Molecular Dynamics Simulations on Coalescence and Non-coalescence of Conducting Droplets

When an electric field with various strengths is applied to two adjacent conducting droplets, the droplets may completely coalesce, partially coalesce, or bounce off one another. To reveal an atom-scale mechanism of coalescence or non-coalescence, dynamic behaviors of two conducting nanodroplets at a homogeneous electric field are studied via molecular dynamics simulations in this work. The results show that there is a critical field strength and a critical cone angle above which the two droplets partially coalesce or bounce off. Charge transfer between the two droplets is observed when the droplets are brought into contact. The partial coalescence and the bounce-off of the two droplets at strong field strengths are found to be due to the high charge transfer rate, which leads to the breakup of the coalescing droplet at different locations.

Differentially expressed genes in the fat body of Bombyx mori in response to phoxim insecticide

The silkworm, Bombyx mori, is an economically important insect. However, poisoning of silkworms by organophosphate pesticides causes tremendous loss to the sericulture. The fat body is the major tissue involved in detoxification and produces antimicrobial peptides and regulates hormones. In this study, a microarray system comprising 22,987 oligonucluotide 70-mer probes was employed to examine differentially expressed genes in the fat body of B. mori exposed to phoxim insecticide. The results showed that a total of 774 genes were differentially expressed upon phoxim exposure, including 500 up-regulated genes and 274 down-regulated genes. The expression levels of eight detoxification-related genes were up-regulated upon phoxim exposure, including six cytochrome P450s and two glutathione-S-transferases. It was firstly found that eight antimicrobial peptide genes were down-regulated, which might provide important references for studying the larvae of B. mori become more susceptible to microbial infections after phoxim treatment. In addition, we firstly detected the expression level of metamorphosis-related genes after phoxim exposure, which may lead to impacted reproduction. Our results may facilitate the overall understanding of the molecular mechanism of multiple pathways following exposure to phoxim insecticide in the fat body of B. mori.

Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation

Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.

Major histocompatibility complex class II polymorphisms in forest musk deer (Moschus berezovskii) and their probable association with purulent disease

Genes of the major histocompatibility complex (MHC) family are crucial in immune responses because they present pathogenic peptides to T cells. In this study, we analysed the genetic variation in forest musk deer (Moschus berezovskii) MHC II genes and its potential association with musk deer purulent disease. In total, 53 purulent disease-susceptible and 46 purulent disease-resistant individuals were selected for MHC II exon 2 fragment analysis. Among them, 16 DQ alleles and four additional DR alleles were identified, with DQ exon 2 fragments displaying a low level of polymorphism. The nonsynonymous substitutions exceeded the synonymous substitutions in the peptide-binding sites of DQA2, DQB1 and DQB2. Then, 28 MHC II alleles were used to analyse the distribution patterns of purulent disease between the susceptible and resistant groups. Among them, three alleles (DQA1*01, DQA1*02 and DQA2*04) were found to be resistant, and five alleles (DRB3*07, DQA1*03, DQA1*04, DQA2*05 and DQA2*06) were found to increase susceptibility. Additionally, three haplotypes were found to be putatively associated with musk deer purulent disease. However, these three haplotypes were only found in the resistant or susceptible group, and their frequencies were low. The results from our study support a contributory role of MHC II polymorphisms in the development of purulent disease in forest musk deer.

Characteristics of phoxim-exposed gene transcription in the silk gland of silkworms

Silkworm (Bombyx mori), a model Lepidoptera insect, is an important economic insect. Its silk gland is the important organ for silk protein synthesis and secretion. Phoxim exposure causes deficient cocooning of silkworm and has become one of the major negative factors for the silk industry. To study the impact of phoxim exposure on silk gland, using gene chip technology, we examined differentially expressed genes in silk gland after silkworms were exposed to phoxim (4.0μg/mL) for 24h. Functional annotation, classification and KEGG signaling pathway analysis were performed. The results showed that out of 3206 genes detected in silk gland after phoxim exposure, 270 were differentially expressed significantly, including 249 up-regulated genes and 21 down-regulated genes. These differentially expressed genes related to apoptosis, detoxification and protein degradation were selected. Using qRT-PCR, the expression levels of 9 genes involved in apoptosis, detoxification and protein degradation were validated. In addition, the expression profiles of three related fibroin synthesis genes (Fib-H, Fib-L and P25) were analyzed. Our results showed that phoxim exposure induced apoptosis of silk gland cells and inhibition of fibroin synthesis. This may be the cause of deficient silkworm cocooning.

Changes in the activity and the expression of detoxification enzymes in silkworms (Bombyx mori) after phoxim feeding

Silkworm (Bombyx mori) is an economically important insect. However, non-cocoon caused by chemical insecticide poisoning has largely hindered the development of sericulture. To explore the roles of detoxification enzymes in B. mori after insecticide poisoning, we monitored the activity changes of cytochrome P450 monooxygenase, glutathione-S-transferase, and carboxylesterase in B. mori midgut and fatbody after phoxim feeding. At the same time, the expression levels of detoxification enzyme-related genes were also determined by real-time quantitative PCR. Compare to the control levels, the activity of P450 in the midgut and fatbody was increased to 1.72 and 6.72 folds; the activity of GST was no change in midgut, and in fatbody increased to 1.11 folds; the activity of carboxylesterase in the midgut was decreased to 0.69 folds, and in fatbody increased to 1.13 folds. Correspondingly, the expression levels of detoxifying enzyme genes CYP6ae22, CYP9a21, GSTo1 and Bmcce were increased to 15.99, 3.32, 1.86 and 2.30 folds in the midgut and to 3.58, 1.84, 2.14 and 4.21 folds in the fatbody after phoxim treatment. These results demonstrated the important roles of detoxification enzymes in phoxim metabolism. In addition, the detected activities of such enzymes were generally lower than those in cotton bollworms (Helicoverpa armigera), which may contribute to the high susceptibility of B. mori to insecticides. Our findings laid the foundation for further investigations of the molecular mechanisms of organophosphorus pesticide metabolism in B. mori.

Transcriptional characteristics of gene expression in the midgut of domestic silkworms (Bombyx mori) exposed to phoxim

Silkworm (Bombyx mori) is not only an economically important insect but also a model system for lepidoptera. As a vital organ of digestion and nutrient absorption, the midgut of insects also serves as the first physiological barrier to chemical pesticides. In this study, microarray was performed to profile the gene expression changes in the midgut of silkworms exposed to phoxim. After 24h of phoxim exposure (4.0μg/mL), 266 genes displayed at least 2.0-fold changes in expression levels. Among them, 192 genes were up-regulated, and 74 genes were down-regulated. The most significant changes were 14.88-fold up-regulation and 23.36-fold down-regulation. According to gene ontology annotation and pathway analysis, differentially expressed genes were mainly classified into different groups based on their potential involvements in detoxification, immunne response, stress response, energy metabolism and transport. Particularly, the transcription levels of detoxification-related genes were up-regulated, such as cytochrome P450s, esterases and glutathione-S-transferase (GST), indicating increased detoxification activity in the midgut. Our study provides new insights into the molecular mechanism of pesticide metabolism in the midgut of insects, which may promote the development of highly efficient insecticides.

Peripheral blood mRNA expression patterns to differentiate hepatocellular carcinoma from other hepatic diseases

Peripheral blood genes expressions profiling (GeXP) have been convinced to be more specific for the diagnosis of cancer and other diseases, and the GeXP system provides an ideal method to analyze multiple genes expression in one normalized and equable system. We aim to differentiate hepatocellular carcinoma from other hepatic diseases based on peripheral blood and the GeXP system. Fifteen selected hepatic diseases related genes with two house-keeping genes for normalization were detected by the GeXP system. The diagnosis model was based on K nearest neighbor classifier and cross validation, and software based on MATLAB software was built for differential diagnosis of hepatic diseases. Eight hepatic related genes were demonstrated to show an obvious statistic difference in expressions while the K nearest neighbors classifier showed that the accuracy for normal controls, hepatitis B, liver cirrhosis, hepatocellular carcinoma and the Other group was separately 80.57 %, 78.17 %, 84.48 %, 73.24 % and 85.85 %. The set of validation has been carried out to assess the accuracy of Model Two and the accuracy was even higher than the set of building for the model, except for the hepatitis B (HBV) group. A sensitive and specific GeXP system of eight genes has been developed for the accurate differential diagnosis of hepatic disease.

Peripheral blood mRNA expression patterns to differentiate hepatocellular carcinoma from other hepatic diseases

Peripheral blood genes expressions profiling (GeXP) have been convinced to be more specific for the diagnosis of cancer and other diseases, and the GeXP system provides an ideal method to analyze multiple genes expression in one normalized and equable system. We aim to differentiate hepatocellular carcinoma from other hepatic diseases based on peripheral blood and the GeXP system. Fifteen selected hepatic diseases related genes with two house-keeping genes for normalization were detected by the GeXP system. The diagnosis model was based on K nearest neighbor classifier and cross validation, and software based on MATLAB software was built for differential diagnosis of hepatic diseases. Eight hepatic related genes were demonstrated to show an obvious statistic difference in expressions while the K nearest neighbors classifier showed that the accuracy for normal controls, hepatitis B, liver cirrhosis, hepatocellular carcinoma and the Other group was separately 80.57 %, 78.17 %, 84.48 %, 73.24 % and 85.85 %. The set of validation has been carried out to assess the accuracy of Model Two and the accuracy was even higher than the set of building for the model, except for the hepatitis B (HBV) group. A sensitive and specific GeXP system of eight genes has been developed for the accurate differential diagnosis of hepatic disease.

The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.

Photochemical decomposition of perfluorodecanoic acid in aqueous solution with VUV light irradiation

The photochemical decomposition of perfluorodecanoic acid (PFDeA) in water in the presence of persulfate ion (S(2)O(8)(2-)) and sulfur ion (S(2-)) was investigated under vacuum ultraviolet (VUV) light irradiation. PFDeA was decomposed under VUV light irradiation. With the addition of S(2)O(8)(2-) or S(2-), the photo-decomposition and defluorination of PFDeA were enhanced significantly. Sulfate radical anion (SO(4)(*-)) generated from photolysis of S(2)O(8)(2-) initiated PFDeA oxidation. While the S(2-) ion, acting as a *OH scavenger, enhanced the role of reduction pathway induced by aqueous electrons (e(aq)(-)). The shorter-chain perfluorocarboxylic acids (PFCAs), formed in a stepwise manner from longer-chain PFCAs, were identified as products by HPLC/MS.

Photochemical decomposition of perfluorooctanoic acid in aqueous periodate with VUV and UV light irradiation

The photochemical decomposition of perfluorooctanoic acid (PFOA) in aqueous periodate (IO(4)(-)) was investigated under two types of low-pressure mercury lamps: one emits at 254nm light (UV light) and the other emits both 254 nm and 185 nm light (VUV light). PFOA decomposed efficiently under VUV light irradiation while it decomposed poorly under UV light irradiation. The addition of IO(4)(-) significantly increased the rate of decomposition and defluorination of PFOA irradiated with UV light whereas it decreased both processes under VUV irradiation. Reactive radical (IO(3)) generated by photolysis of IO(4)(-) initiated the oxidation of PFOA in UV process. Aquated electrons (e(aq)(-)), generated from water homolysis, scavenged IO(4)(-) resulting in decrease of reactive radical species production and PFOA decomposition. The shorter-chain perfluorocarboxylic acids (PFCAs) formed in a stepwise manner from long-chain PFCAs.

Utility of PDL progenitors for in vivo tissue regeneration: a report of 3 cases

OBJECTIVE

Periodontal disease is an inflammatory disorder with widespread morbidities involving both oral and systemic health. The primary goal of periodontal treatment is the regeneration of the lost or diseased periodontium. In this study, we retrospectively examined feasibility and safety of reconstructing the periodontal intrabony defects with autologous periodontal ligament progenitor (PDLP) implantation in three patients.

MATERIALS AND METHODS

In this retrospective pilot study, we treated 16 teeth with at least one deep intrabony defect of probing depth (PD) > OR = 6 mm with PDLP transplantation and evaluated clinical outcome measures in terms of probing depth, gingival recession and attachment gain for a duration of 32-72 months. Furthermore, we compare PDLPs with standard PDL stem cells (PDLSCs) and confirmed that PDLPs possessed progenitor characters.

RESULTS

Clinical examination indicated that transplantationof PDLPs may provide therapeutic benefit for the periodontal defects. All treated patients showed no adverse effects during the entire course of follow up. We also found that PDLPs were analogous to PDLSCs in terms of high proliferation, expression of mesenchymal surface molecules, multipotent differentiation, and in vivo tissue regain. However, PDLPs failed to express scleraxis, a marker of tendon, as seen in PDLSCs.

CONCLUSIONS

This study demonstrated clinical and experimental evidences supporting a potential efficacy and safety of utilizing autologous PDL cells in the treatment of human periodontitis.

Structure effects in angle-resolved high-order above-threshold ionization of molecules

We present energy-resolved angular distributions of photoelectrons generated in above-threshold ionization (ATI) of nonaligned diatomic molecules N2 and O2 in high-intensity short laser pulses, with emphasis on the most energetic part of the spectra. The angular distribution for photoelectrons with energy of 10U(p) (U(p): ponderomotive energy), i.e., the plateau cutoff in ATI spectra, is found to be broader in O2 than in N2. Resorting to the analyses from both an S-matrix theory and an intuitive semiclassical model, we attribute the observation to the effect of the ground state molecular orbital structure on high-energy electron emission in strong-field molecular ionization.

Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes

BACKGROUND

Although originally thought to be less frequent in plants than in animals, alternative splicing (AS) is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt) and Lotus japonicus (Lj).

RESULTS

Based on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (approximately 10%, 1,107 genes) and Lj (approximately 3%, 92 genes) than in Arabidopsis and rice (both around 20%). However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%), with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species.

CONCLUSION

This study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula

The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.

Self-assembly and supramolecular transition of poly(amidoamine) dendrons focally modified with aromatic chromophores

Three novel series of amphiphiles based on poly(amidoamine) dendrons (from G1 to G3) and having different aromatic chromophores (Cz I, Cz II, and Py) at the focal point were synthesized and studied for their self-assembly behavior in aqueous solution by using electronic microscopies (i.e., SEM and TEM), UV-vis, fluorescence, IR, and (1)H NMR spectroscopy. It was found that the generation of dendrons affected significantly the self-assembly of these amphiphiles in aqueous solution and the morphological structures of the resulting assemblies depended greatly on the architecture of the focal chromophores. As a result, the first generation of dendrons assembled readily into vesicles at low concentrations. These vesicular structures subsequently fused to form a stable tubular structure. Similar tubular structures could also be directly obtained through self-assembly of these amphiphilic dendrons at high concentrations. X-ray investigations showed that the resulting tubules possessed a lamellar structure. A head-to-head packing model of amphiphilic dendrons in the assemblies was proposed.

Genomewide comparative analysis of alternative splicing in plants

Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of posttranscriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).