cGAS-STING pathway mediates activation of dendritic cell sensing of immunogenic tumors.

Type I interferons (IFN-I) play pivotal roles in tumor therapy for three decades, underscoring the critical importance of maintaining the integrity of the IFN-1 signaling pathway in radiotherapy, chemotherapy, targeted therapy, and immunotherapy. However, the specific mechanism by which IFN-I contributes to these therapies, particularly in terms of activating dendritic cells (DCs), remains unclear. Based on recent studies, aberrant DNA in the cytoplasm activates the cyclic GMP-AMP synthase (cGAS)- stimulator of interferon genes (STING) signaling pathway, which in turn produces IFN-I, which is essential for antiviral and anticancer immunity. Notably, STING can also enhance anticancer immunity by promoting autophagy, inflammation, and glycolysis in an IFN-I-independent manner. These research advancements contribute to our comprehension of the distinctions between IFN-I drugs and STING agonists in the context of oncology therapy and shed light on the challenges involved in developing STING agonist drugs. Thus, we aimed to summarize the novel mechanisms underlying cGAS-STING-IFN-I signal activation in DC-mediated antigen presentation and its role in the cancer immune cycle in this review.

OsOFP6 Overexpression Alters Plant Architecture, Grain Shape, and Seed Fertility.

OVATE family proteins (OFPs) play important roles in plant growth and development, hormone signaling, and stress response pathways. However, the functions of OsOFPs in rice are largely unknown. In this study, a novel gain-of-function rice mutant, Osofp6-D, was identified. This mutant exhibited decreased plant height, erect leaves, reduced panicle size, short and wide seeds, delayed seed germination time, and reduced fertility. These phenotypic changes were attributed to the increased expression of OsOFP6, which was caused by a T-DNA insertion. Complementation of the Osofp6-D phenotype by knockout of OsOFP6 using the CRISPR/Cas9 system confirmed that the Osofp6-D phenotype was caused by OsOFP6 overexpression. In addition, transgenic plants overexpressing OsOFP6 with the 35S promoter mimicked the Osofp6-D phenotype. Cytological observations of the glumes showed that OsOFP6 overexpression altered the grain shape, mainly by altering the cell shape. Hormone response experiments showed that OsOFP6 was involved in the gibberellin (GA) and brassinolide (BR) signaling responses. Further studies revealed that OsOFP6 interacts with E3BB, which is orthologous to the Arabidopsis central organ size-control protein BIG BROTHER (BB). This study further elucidates the regulation mechanism of the rice OFP family on plant architecture and grain shape.

The Dilemma of HSV-1 Oncolytic Virus Delivery: The Method Choice and Hurdles.

Oncolytic viruses (OVs) have emerged as effective gene therapy and immunotherapy drugs. As an important gene delivery platform, the integration of exogenous genes into OVs has become a novel path for the advancement of OV therapy, while the herpes simplex virus type 1 (HSV-1) is the most commonly used. However, the current mode of administration of HSV-1 oncolytic virus is mainly based on the tumor in situ injection, which limits the application of such OV drugs to a certain extent. Intravenous administration offers a solution to the systemic distribution of OV drugs but is ambiguous in terms of efficacy and safety. The main reason is the synergistic role of innate and adaptive immunity of the immune system in the response against the HSV-1 oncolytic virus, which is rapidly cleared by the body's immune system before it reaches the tumor, a process that is accompanied by side effects. This article reviews different administration methods of HSV-1 oncolytic virus in the process of tumor treatment, especially the research progress in intravenous administration. It also discusses immune constraints and solutions of intravenous administration with the intent to provide new insights into HSV-1 delivery for OV therapy.

The role of PPR proteins in posttranscriptional regulation of organelle components in plants.

Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. They are sequence-specific RNA-binding proteins and play key roles in posttranscriptional processes within organelles. Their combined actions have profound effects on chloroplast photosynthetic electron transport chain and mitochondrial respiratory chain, affecting photosynthesis and respiration respectively, and ultimately on yield, fertility, and grain quality. Over the past decade, much has been learned about the molecular functions of these proteins on plant growth and development. However, due to the large size of this protein family, the functions of most members remain largely unknown. Here, we summarize the molecular mechanisms of PPR proteins functions on organelle genes, and effects on development of organelles and plants. Problems that need to be resolved are also identified. This article will provide a theoretical basis for understanding the functions of PPR protein family and genetic improvements of grain yield and quality.

Identification of stable QTLs causing chalk in rice grains in nine environments.

KEY MESSAGE: A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

Comparison of percutaneous transhepatic biliary drainage and endoscopic biliary drainage in the management of malignant biliary tract obstruction: a meta-analysis.

BACKGROUND AND AIM: To compare percutaneous transhepatic biliary drainage (PTBD) and endoscopic biliary drainage (EBD) for management of malignant biliary tract obstruction (MBTO). METHODS: PubMed, Google Scholar, and the Cochrane database were searched to 31 December 2013. Main outcome measurements were therapeutic success rate, 30-day mortality rate, overall complications, cholangitis, and pancreatitis. RESULTS: Eight studies (five retrospective and three randomized controlled trials) were included in the meta-analysis with a total of 692 participants. Combined odds ratio (OR) = 2.18 revealed no significant difference in therapeutic success between PTBD and EBD (95% confidence interval [CI] = 0.73-6.47, P = 0.162). However, after excluding two studies that appeared to be outliers, PTBD exhibited a better therapeutic success rate than EBD (pooled OR = 4.45, 95% CI = 2.68-7.40, P < 0.001). Patients who underwent PTBD were 0.55 times as likely to have cholangitis as those who underwent EBD, whereas the overall complication rate, pancreatitis rate, and 30-day mortality were similar between the two procedures. CONCLUSIONS: PTBD may be associated with a better therapeutic success rate and lower incidence of cholangitis than EBD, but the overall complication rate, pancreatitis rate, and 30-day mortality of the two procedures are similar.

A modified HSV-1 oncolytic virus reconciles antiviral and antitumor immunity via promoting IFNß expression and inhibiting PKR.

Type I interferon (IFN-I) is a potent immune modulator intricately involved in regulating tumor immunity. Meanwhile, the integrity of the IFN-I signaling pathway is essential for radiotherapy, chemotherapy, targeted therapy, and immunotherapy. However, the clinical application of IFN-I remains challenging due to its non-specific cytotoxicity and limited half-life. To overcome these limitations, we developed a gene delivery platform, CRISPR-V, enabling the rapid creation of novel HSV-1 oncolytic viruses. Utilizing this platform, we created an oncolytic virus, OVH-IFNß, in which the IFNß gene was incorporated into the HSV-1 genome. However, exogenous IFNß expression significantly inhibited OVH-IFNß replication. Through transcriptome data analyses, we identified several ISG genes inhibiting OVH-IFNß replication. By gene knockout and functional studies of the downstream effectors, we confirmed the prominent antiviral activities of protein kinase R (PKR). To balance the antitumor and antiviral immunity of IFNß, we developed a novel HSV-1 oncolytic virus, OVH-IFNß-iPKR, which can express IFNß while inhibiting PKR, leading to a potent antitumor immunity while reducing the antiviral capacity of IFNß. OVH-IFNß-iPKR shows a strong ability to induce immunogenic cell death and activate tumor-specific CD8+ T cells, leading to de novo immune responses and providing a novel strategy for tumor immunotherapy.

Spectral properties inspired image enhancement for crystalline polymer powder impurity detection.

Crystalline polymer powder inevitably incorporates certain impurities, including decomposed polymers or foreign particles. An essential criterion for assessing the quality of polymers is the quantity of contaminants in the powder. However, it is challenging to discern powder contaminants through machine vision due to the poor quality of images taken at production sites. Inspired by the spectral properties of crystalline polymers, this paper proposes an efficient image-based impurity detection method, which seeks to precisely and robustly detect contaminant content. Based on the changes in absorbance during polymer decomposition, a highly selective channel-weighted image enhancement approach is designed to emphasize the difference between impurities and normal particles. Then, using the prior information on the powder's attributes, an adaptive thresholding method is employed to categorize pixels belonging to impurities. Finally, a dataset of 119 12-megapixel photos from a chemical facility, where the average size of contaminants in images is 43 pixels, is used to evaluate the performance of the proposed algorithm. The results of the detection demonstrate that the proposed strategy for image enhancement has better selectivity to impurities than typical image enhancement methods.

CXCL1 promotes colon cancer progression through activation of NF-κB/P300 signaling pathway.

BACKGROUND: The upregulated expression of CXCL1 has been validated in colorectal cancer patients. As a potential biotherapeutic target for colorectal cancer, the mechanism by which CXCL1 affects the development of colorectal cancer is not clear. METHODS: Expression data of CXCL1 in colorectal cancer were obtained from the GEO database and verified using the GEPIA database and the TIMER 2.0 database. Knockout and overexpression of CXCL1 in colorectal cancer cells by CRISPR/Cas and "Sleeping Beauty" transposon-mediated gene editing techniques. Cell biological function was demonstrated by CCK-8, transwell chamber and Colony formation assay. RT-qPCR and Western Blot assays measured RNA and protein expression. Protein localization and expression were measured by immunohistochemistry and immunofluorescence. RESULTS: Bioinformatics analysis showed significant overexpression of CXCL1 in the colorectal cancer tissues compared to normal human tissues, and identified CXCL1 as a potential therapeutic target for colorectal cancer. We demonstrate that CXCL1 promotes the proliferation and migration of colon cancer cells and has a facilitative effect on tumor angiogenesis. Furthermore, CXCL1 elevation promoted the migration of M2-tumor associated macrophages (TAMs) while disrupting the aggregation of CD4+ and CD8+ T cells at tumor sites. Mechanistic studies suggested that CXCL1 activates the NF-κB pathway. In the in vivo colon cancer transplantation tumor model, treatment with the P300 inhibitor C646 significantly inhibited the growth of CXCL1-overexpressing colon cancer. CONCLUSION: CXCL1 promotes colon cancer development through activation of NF-κB/P300, and that CXCL1-based therapy is a potential novel strategy to prevent colon cancer development.

Prognostic factors for patients with mass-forming intrahepatic cholangiocarcinoma: A case series of 68 patients.

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer in humans after hepatocellular carcinoma and a rare epithelial malignancy that results in a poor prognosis. According to the Liver Cancer Study Group of Japan classification, ICC can be divided into three types: Mass-forming (MF) type, periductal-infiltrating (PI) type, and intraductal-growth type. The MF type is the most common, accounting for 57.1-83.6% of ICCs. Nevertheless, little is known about the epidemiology and treatment of MF ICC. AIM: To examine the prognostic factors for patients with MF ICC. METHODS: We carried out a retrospective analysis of consecutive patients with MF ICC treated at the Faculty of Hepato-Pancreato-Biliary Surgery of Chinese PLA General Hospital between January 2008 and December 2018. According to the treatment received, the patients were divided into either a resection group or an exploration group. RESULTS: The pooled 1-, 3-, and 5-year survival rates in the 68 patients with MF ICC were 66.5%, 36.3%, and 9.3%, respectively. Univariate analysis revealed that surgical resection (P < 0.001), nodal metastasis (P < 0.001), tumor location (P = 0.039), vascular invasion (P < 0.001), ascites (P < 0.001), and differentiation (P = 0.009) were significantly associated with the prognosis and survival of MF ICC. Multivariate analysis revealed that ascites (hazard ratio [HR] = 5.6, 95% confidence interval [CI]: 1.6-18.9, P = 0.006) and vascular invasion (HR = 2.5, 95%CI: 1.0-6.1, P = 0.045) were independent risk factors for MF ICC. The pooled 1-, 3-, and 5-year survival rates in the 19 patients of the exploration group were 5.3%, 5.3%, and 0, respectively. Among the 49 patients who underwent surgical resection, the pooled 1-, 3-, and 5-year survival rates were 93.5%, 49.7%, and 14.4%, respectively. Univariate and multivariate analyses revealed that vascular invasion (HR = 3.1, 95%CI: 1.2-8.5, P = 0.024) and nodal metastasis (HR = 3.2, 95%CI: 1.4-7.6, P = 0.008) were independent prognostic risk factors for surgical resection patients. CONCLUSION: The prognosis of MF ICC patients is dismal, especially those with ascites or vascular invasion. Surgical resection is a key factor in improving overall survival in patients with MF ICC, and vascular invasion and lymph node metastasis affect the efficacy of surgical resection.

Effects of drought stress and elevated CO2 on starch fine structures and functional properties in indica rice.

The changes in rice starch fine structures and functional properties induced by drought, elevated CO2 (eCO2) and combined treatments remain to be elucidated comprehensively. In this study, starch molecular structures were characterized by size-exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis, and the data from amylopectin chain-length distributions was fitted with a mathematical model to obtain parameters for statistical analysis. Starch crystalline structures, thermal and pasting properties of rice flour were also analyzed. All the treatments decreased the seed setting rate and increased chalky grains, reflecting the abnormal starch accumulation. However, eCO2 partially increased the seed setting rate and chalky grains under drought stress. The stress-treated starch samples had shorter amylopectin short and intermediate chains, the lower degree of ordered structures, but similar amylose content and relative crystallinity. This led to lower onset gelatinization temperature and paste viscosities, which may be responsible for the worse sensory quality of rice grains.

Feasibility and safety of "bridging" pancreaticogastrostomy for pancreatic trauma in Landrace pigs.

BACKGROUND: In recent years, we created and employed a new anastomosis method, "bridging" pancreaticogastrostomy, to treat patients with extremely severe pancreatic injury. This surgery has advantages such as short length of surgery, low secondary trauma, rapid construction of shunts for pancreatic fluid, preventing second surgeries, and achieving good treatment outcomes in clinical practice. However, due to the limited number of clinical cases, there is a lack of strong evidence to support the feasibility and safety of this surgical procedure. Therefore, we carried out animal experiments to examine this procedure, which is reported here. AIM: To examine the feasibility and safety of a new rapid method of pancreaticogastrostomy, "bridging" pancreaticogastrostomy. METHODS: Ten Landrace pigs were randomized into the experimental and control groups, with five pigs in each group. "Bridging" pancreaticogastrostomy was performed in the experimental group, while routine mucosa-to-mucosa pancreaticogastrostomy was performed in the control group. After surgery, the general condition, amylase levels in drainage fluid on Days 1, 3, 5, and 7, fasting and 2-h postprandial blood glucose 6 mo after surgery, fasting, 2-h postprandial peripheral blood insulin, and portal vein blood insulin 6 mo after surgery were assessed. Resurgery was carried out at 1 and 6 mo after the former one to examine the condition of the abdominal cavity and firmness and tightness of the pancreaticogastric anastomosis and pancreas. RESULTS: After surgery, the general condition of the animals was good. One in the control group did not gain weight 6 mo after surgery, whereas significant weight gain was present in the others. There were significant differences on Days 1 and 3 after surgery between the two groups but no differences on Days 5 and 7. There were no differences in fasting and 2-h postprandial blood glucose and fasting and 2-h insulin values of postprandial peripheral blood and portal vein blood 6 mo after surgery between the two groups. One month after surgery, the sinus tract orifice/anastomosis was patent in the two groups. Six months after surgery, the sinus tract orifice/anastomosis was sealed, and pancreases in both groups presented with chronic pancreatitis. CONCLUSION: "Bridging" pancreaticogastrostomy is a feasible and safe a means of damage control surgery during the early stage of pancreatic injury.

Generation of Marker-Free Transgenic Rice Resistant to Rice Blast Disease Using Ac/Ds Transposon-Mediated Transgene Reintegration System.

Rice blast is one of the most serious diseases of rice and a major threat to rice production. Breeding disease-resistant rice is one of the most economical, safe, and effective measures for the control of rice blast. As a complement to traditional crop breeding, the transgenic method can avoid the time-consuming process of crosses and multi-generation selection. In this study, maize (Zea mays) Activator (Ac)/Dissociation (Ds) transposon vectors carrying green fluorescent protein (GFP) and red fluorescent protein (mCherry) genetic markers were used for generating marker-free transgenic rice. Double fluorescent protein-aided counterselection against the presence of T-DNA was performed together with polymerase chain reaction (PCR)-based positive selection for the gene of interest (GOI) to screen marker-free progeny. We cloned an RNAi expression cassette of the rice Pi21 gene that negatively regulates resistance to rice blast as a GOI into the Ds element in the Ac/Ds vector and obtained marker-free T1 rice plants from 13 independent transgenic lines. Marker-free and Ds/GOI-homozygous rice lines were verified by PCR and Southern hybridization analysis to be completely free of transgenic markers and T-DNA sequences. qRT-PCR analysis and rice blast disease inoculation confirmed that the marker-free transgenic rice lines exhibited decreased Pi21 expression levels and increased resistance to rice blast. TAIL-PCR results showed that the Ds (Pi21-RNAi) transgenes in two rice lines were reintegrated in intergenic regions in the rice genome. The Ac/Ds vector with dual fluorescent protein markers offers more reliable screening of marker-free transgenic progeny and can be utilized in the transgenic breeding of rice disease resistance and other agronomic traits.

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice.

BACKGROUND: The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice. RESULTS: We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis. CONCLUSIONS: In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

[Determinants of long-term survival after pancreaticoduodenectomy for ampulla of Vater carcinoma].

OBJECTIVE: To investigate the determinants of long-term survival for ampulla of Vater carcinoma treated by pancreaticoduodenectomy. METHODS: A total of 77 patients with ampulla of Vater carcinoma undergoing pancreaticoduodenectomy were reviewed. Kaplan-Meier method was used to analyze the survival rate. Independent t test was used for statistical comparison and COX regression model for multivariate analysis. RESULTS: No patient died as a result of surgery. The overall 5-year survival was 40.7%. Univariate analysis showed that perioperative serum carcinoembryonic antigen (CEA) level (P = 0.012), tumor invasion depth (P = 0.000), UICC stage (P = 0.000) and tumor size (P = 0.001) were significant prognostic factors of ampulla of Vater carcinoma; in multivariate analysis, only the tumor size (P = 0.000) was an independent prognostic factor of ampulla of Vater carcinoma. CONCLUSION: Pancreaticoduodenectomy is associated with significant survival. Tumor size is the most important influencing factor of outcome after pancreaticoduodenectomy; in addition, perioperative serum CEA level, tumor invasion depth and UICC stage may also influence the survival rate, there exists a need for further follow-up studies.

[Experience from surgical resection for 48 cases of hilar cholangiocarcinoma].

OBJECTIVE: To summarize the methods, safety and efficiency of surgical resection for hilar cholangiocarcinoma. METHODS: The clinical and follow-up data of 48 patients with hilar cholangiocarcinoma underwent surgical resection from January 2003 to December 2007 were analyzed retrospectively. There were 26 male and 22 female, aged from 38 to 72 years old with a mean of 63.6 years old. RESULTS: Perioperative management including percutaneous transhepatic biliary drainage applied in 19 cases and portal vein embolization applied in 2 cases. Eight patients were treated with extrahepatic bile duct resection with or without parital hepatic segment II resection, 10 cases with perihilar hepatic resection (segment IVB, partial V, partial VIII, I), 28 cases with extended hemihepatectomy and 2 cases with central hepatic resection (segment IVB, V, VIII, I). R0 resection rate was 89.5% and the operative mortality was 2.1%. The 1-, 3- and 5-year survival rate were 93.5%, 51.8% and 36.5%, respectively. Patients undergoing extended hepatic resection survived significantly longer than those undergoing partial hepatic resection (P = 0.034). CONCLUSIONS: Extended hepatic resection for hilar cholangiocarcinoma offers good outcomes with an acceptable mortality rate.

A novel prognostic score model based on combining systemic and hepatic inflammation markers in the prognosis of HBV-associated hepatocellular carcinoma patients.

Objectives: The study aimed to evaluate the prognostic value of systemic inflammation markers [neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), Prognostic Nutritional Index (PNI)] and hepatic inflammation markers [aspartate aminotransferase-to-platelet ratio index (APRI), γ-glutamyl transferase (γ-GT)/alanine aminotransferase (ALT)] in patients with hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) and further to develop a novel prognostic score model. Methods: A total of 401 cases with HBV-associated HCC who underwent hepatectomy as initial therapy were included in the analysis. Kaplan-Meier was performed to construct survival curves and receiver operating characteristic (ROC) analysis was used to detect the optimal cut-off value of markers. The prognostic score model was constructed using significant inflammation markers in the Cox model. Each factor was given a score of 1 and patients were stratified according to the scores. Results: In the Cox model, α-fetoprotein (AFP), ALT, tumour differentiation, maximum size of tumours, TNM stage, PNI and γ-GT/ALT were independently prognostic factors. We established a preoperative inflammation-based prognostic scoring model combining PNI and γ-GT/ALT. The novel preoperative inflammation-based prognostic score was superior (area under the curve [AUC], 0.659) to 7th tumour-node-metastasis (TNM) stage (AUC, 0.600) despite no statistical significance (p = .1036). Conclusion: PNI and γ-GT/ALT are independent predictors for prognosis. The novel prognostic score model based on systemic and hepatic inflammation markers is suitable for the prognosis evaluation in patients with HBV-associated HCC.

Development of microsatellite markers and construction of genetic map in rice blast pathogen Magnaporthe grisea.

Magnaporthe grisea is the most destructive fungal pathogen of rice and a model organism for studying plant-pathogen interaction. Molecular markers and genetic maps are useful tools for genetic studies. In this study, based on the released genome sequence data of M. grisea, we investigated 446 simple sequence repeat (SSR) loci and developed 313 SSR markers, which showed polymorphisms among nine isolates from rice (including a laboratory strain 2539). The number of alleles of each marker ranged 2-9 with an average of 3.3. The polymorphic information content (PIC) of each marker ranged 0.20-0.89 with an average of 0.53. Using a population derived from a cross between isolates Guy11 and 2539, we constructed a genetic map of M. grisea consisting of 176 SSR markers. The map covers a total length of 1247 cM, equivalent to a physical length of about 35.0 Mb or 93% of the genome, with an average distance of 7.1cM between adjacent markers. A web-based database of the SSR markers and the genetic map was established (http://ibi.zju.edu.cn/pgl/MGM/index.html).

PIP: a database of potential intron polymorphism markers.

MOTIVATION: With the recent progress made in large-scale plant functional genome sequencing projects, a great amount of EST (express sequence tag) data is becoming available. With the help of complete genomic sequence information of model plants (rice and Arabidopsis), it is possible to predict the joints between adjacent exons after splicing (or termed 'intron positions' for short) in homologous ESTs of other plants. This would allow developing potential intron polymorphism (PIP) markers in these plants by designing primers in exons flanking the target intron. RESULTS: We have extracted a total of 57,658 PIP markers in 59 plant species and created a web-based database platform named PIP to provide detailed information of these PIP markers and homologous relationships among PIP markers from different species. The platform also provides a function of online designing of PIP markers based on cDNA/EST sequences submitted by users. With evaluations performed in silico, we have found that the intron position prediction is highly reliable and the polymorphism level of PIP markers is high enough for practical need. AVAILABILITY: http://ibi.zju.edu.cn/pgl/pip/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Construction of a genetic map based on ILP markers in rice].

Intron length polymorphism (ILP) is a new type of PCR-based molecular markers with many advantages. We had previously developed 172 ILP markers in rice using the published genome sequence data of indica cultivar 93-11 and ja-ponica cultivar Nipponbare. In order to examine the reliability and the applicability of these ILP markers to genetic map-ping, we constructed a rice genetic map consisting of 172 ILP and 13 SSR markers with a total length of 1 905.7 cM using a BC1F1 (Nipponbare/93-11//Nipponbare) population. Comparison showed that the order of the markers in this map was ex-actly the same as their physical order, verifying the feasibility and efficiency of using ILP markers for genetic mapping. We also investigated the phenomenon of marker segregation distortion and found a region of serious segregation distortion in the short arm of chromosome 6.