The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

BACKGROUND: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. METHODS: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. RESULTS: The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. CONCLUSION: Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Targeted association analysis identified japonica rice varieties achieving Na(+)/K (+) homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra.

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na(+) concentration and Na(+)/K(+) equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na(+) concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement.

[An experimental model of transgastric ooforectomy using a porcine model]. / Stabilirea modelului experimental de ooforectomie transgastrica pe model suin.

INTRODUCTION: Transabdominal routes for surgery entail general anaesthesia with its inherent risks and complications (prolonged hospital stay, abdominal incisions that may be difficult in obese patients). Minimally invasive procedures require shorter hospitalization, have shorter recovery periods, less postoperative discomfort, and lower morbidity and complications. The purpose of this study was to use a porcine model to determine the feasibility and the safety of organ resection (oophorectomy and tubectomy). MATERIALS AND METHODS: 10 Big White pigs between 25-30 kg underwent transgastric ooforectomy. The first 5 cases were performed in a hybrid procedure (laparoscopic-NOTES) in order to have a better control and supervise the maneuvers done by the mobile endoscope and to guide in the abdominal cavity. RESULTS: Adnexectomy was possible in all ten experiments. Full operative time (from starting endoscopy to complete gastrectomy closing) was 180 min to 270 min. The gastric defect closing was the most difficult manoever lasting from 10 min with OTSC clips to 100 using endoloops and clips. The animals have tolerated well the experiments and there have been no remarkable incidents during our 10 experments. In only one case a bleeding from gastotomy required electric coagulation. CONCLUSION: Transgastric ooforectomy in an experimental model is a procedure that requires advanced laparoscopical and endoscopical skills. Our early results are promissing. Its application in humans needs further confirmation of the method.

[Liver transplantation--indications, surgical technique, results--the analysis of a clinical series of 200 cases]. / Transplantul hepatic--indicati, tehnica, rezultate-analiza unei serii clinice de 200 de cazuri.

INTRODUCTION: Initially considered experimental, liver transplantation (LT) has become the treatment of choice for the patients with end-stage liver diseases. MATERIAL AND METHODS: Between April 2000 and October 2009, 200 LTs (10 reLTs) were performed in 190 patients, this study being retrospective. There were transplanted 110 men and 80 women, 159 adults and 31 children with the age between 1 and 64 years old (mean age--39.9). The main indication in the adult group was represented by viral cirrhosis, while the pediatric series the etiology was mainly glycogenosis and biliary atresia. There were performed 143 whole graft LTs, 46 living donor LTs, 6 split LTs, 4 reduced LTs and one domino LT RESULTS: The postoperative survival was 90% (170 patients). The patient and graft one-year and five-year survivals were 76.9%, 73.6% and 71%, 68.2%, respectively. The early complications occurred in 127 patients (67%). The late complications were recorded in 71 patients (37.3%). The intraoperative and early postoperative mortality rate was 9.5% (18 patients). CONCLUSIONS: The Romanian liver transplantation program from Fundeni includes all types of current surgical techniques and the results are comparable with those from other international centers.

[Anesthesia for experimental surgery in swine]. / Anestezia pentru chirurgia experimentala la porci.

New surgical techniques cannot be safely and widely performed in human subjects unless they are first applied to large animal models. Experimental model using swine as surgical practice subject is one of the most reliable and widely practiced, taking into consideration the similarity between human and swine anatomy. Based on our large experience (around 100 pigs) we hereby present important aspects of handling and anesthesia procedures for pigs. Our goal is to share our experience with young surgical and anesthesia investigators who are planning investigations using pig as an experimental animal.

ARCHIPELAGO: a dedicated resource for exploiting past, present, and future genomic data on disease resistance regulation in rice.

Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice-pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.

OryGenesDB: a database for rice reverse genetics.

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an 'anchoring' option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.

Circulating cardiac troponin T in myocardial contusion.

STUDY OBJECTIVE: Myocardial contusion may induce life-threatening complications, but its diagnosis is difficult. Circulating cardiac troponin T is considered a highly sensitive and specific marker of myocardial cell injury. We investigate the value of cardiac troponin T measurement in the diagnosis of myocardial contusion. DESIGN: Prospective study. SETTING: Level 1 trauma center. METHODS: We prospectively measured circulating cardiac troponin T and performed echocardiography and continuous Holter monitoring in patients who had suffered blunt trauma. Myocardial contusion was diagnosed in patients who fulfilled one of the following criteria: (1) an abnormal echocardiography compatible with myocardial contusion; (2) severe cardiac rhythm abnormalities; (3) severe cardiac conduction abnormalities; and (4) hemopericardium. MEASUREMENTS AND RESULTS: One hundred twenty-eight patients were included and myocardial contusion was diagnosed in 29 patients. Patients with myocardial contusion had more severe trauma, experienced more frequently associated thoracic lesions, and had a lower left ventricular ejection fraction area (48 +/- 15 vs 61 +/- 10%; p < 0.001). Elevated circulating cardiac troponin T concentrations were significantly more frequent in patients with a myocardial contusion (31 vs 9%; p < 0.007). An elevated circulating cardiac troponin T concentration (> or = 0.5 microgram/L) was more accurate than MB fraction of creatine kinase (CK) (CK-MB) and CK-MB/CK ratio in the diagnosis of myocardial contusion, as shown by an area under the receiver operating characteristic (ROC) curve (AROC), which was significantly different from 0.50 (AROC = 0.69; 95% confidence interval, 0.56 to 0.80). However, this improvement was not clinically acceptable (sensitivity, 0.31; specificity, 0.91). CONCLUSIONS: Circulating cardiac troponin T measurement had a slightly greater diagnostic value than usual biological parameters (CK-MB, CK-MB/CK) in myocardial contusion. Nevertheless, it was concluded that an elevated circulating cardiac troponin T concentration has no important clinical value in the diagnosis of myocardial contusion.

[Amputation of the rectum via laparoscopy]. / Amputatie de rect pe cale laparoscopica.

We report the case of a 66-year-old woman with a bleeding adenocarcinoma of the lower thirty of the rectum. The laparoscopic procedure was initiated with mobilization of the sigmoid colon. The left ureter was identified as it crosses the left iliac vessels. The peritoneum along the right side of the rectosigmoid mesentery was transected. The superior rectal artery was divided utilizing extracorporeal ligatures. The anterior rectum was separated from the uterus, the pararectal tissue was mobilized, the middle rectal arteries were ligated and the posterior rectum was dissected from the presacral tissue. The perineal component of the procedure was simultaneously performed. The sigmoid loop was extracorporeally transected with a linear stapler. The proximal sigmoid end was exteriorized through the colostomy site (site of the left superior port). The distal sigmoid end was replaced in the abdominal cavity and was grasped through the perineal wound; the anus, rectum and sigmoid were removed through the perineal wound. The feasibility of this procedure has been well established. However, it seems to be an alternative for the classical abdominoperineal resection as treatment for adenocarcinoma of the lower rectum. His superiority has yet to be confirmed by future studies.

[Liver transplantation--considerations over 8 cases operated in the year 2000]. / Transplantul hepatic--consideratii asupra a 8 cazuri operate în anul 2000.

In the year 2000, at the Department for General Surgery and Liver Transplantation from The Fundeni Clinical Institute Bucharest, seven OLTs and one living-related transplantation were performed in 6 adults and 2 children. Postoperative complications were: bile leakage, hemoperitoneum, lower gastrointestinal hemorrhage, parietoabdominal hematoma. There was only one postoperative death due to septic complications in the 18th p.o.d. and one late death due to pneumonia of unknown origin. After the results in the year 2000 there was an increased number of donors and referrals. We consider that now in Romania this is an established program that will continue depending on the number of donors and financing.

Early and specific gene expression triggered by rice resistance gene Pi33 in response to infection by ACE1 avirulent blast fungus.

* Our view of genes involved in rice disease resistance is far from complete. Here we used a gene-for-gene relationship corresponding to the interaction between atypical avirulence gene ACE1 from Magnaporthe grisea and rice resistance gene Pi33 to better characterize early rice defence responses induced during such interaction. * Rice genes differentially expressed during early stages of Pi33/ACE1 interaction were identified using DNA chip-based differential hybridization and QRT-PCR survey of the expression of known and putative regulators of disease resistance. * One hundred genes were identified as induced or repressed during rice defence response, 80% of which are novel, including resistance gene analogues. Pi33/ACE1 interaction also triggered the up-regulation of classical PR defence genes and a massive down-regulation of chlorophyll a/b binding genes. Most of these differentially expressed genes were induced or repressed earlier in Pi33/ACE1 interaction than in the gene-for-gene interaction involving Nipponbare resistant cultivar. * Besides demonstrating that an ACE1/Pi33 interaction induced classical and specific expression patterns, this work provides a list of new genes likely to be involved in rice disease resistance.