Reconstruction of a Genetic Pathway Using Transcriptome Mapping in a Metazoan

RNA‐seq is a technique that is commonly used to identify downstream elements to a genetic or chemical perturbation. In theory, global transcriptomes contain enough information to perform a full‐fledged genetic analysis of a pathway. Early attempts to do this using microarrays in single celled organisms reported partial reconstruction of a genetic pathway. Using the hypoxia pathway, we show that genetic reconstructions can be performed using global transcriptome data. We obtained the transcriptomes of 5 C. elegans single mutants and 2 double mutants at the young adult stage. We show that in a blinded computational study, we were able to identify relevant genetic relationships between all genes in a pathway. In addition, we identified a core set of ~500 genes that make up the bulk of the C. elegans hypoxia response. Multiple of these genes are directly implicated in the Electron Transport Chain (ETC), metabolism regulation or chemical damage responses

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes

WormBase (www.wormbase.org) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided

Entero-endocrine cell differentiation in carcinomas of the gallbladder and mucinous cystadenocarcinomas of the pancreas

Forty two carcinomas of the gallbladder and 25 mucinous cystadenocarcinomas of the pancreas were analyzed using silver stains and immunohistochemical techniques. Fourteen (33.3%) gallbladder carcinomas had argyrophil and argentaffin cells and 17 (40%) contained endocrine cells as shown by immunoperoxidase stains. The gallbladder tumors that had the largest number of endocrine cells were the well differentiated adenocarcinomas with colonic features. The most common endocrine cell in these tumors was the serotonin-containing (EC) cell followed by somatostatin-containing cells and cells that reacted to pancreatic polypeptide and gastrin. Intestinal metaplasia with pseudopyloric gland hyperplasia was present in the gallbladder mucosa adjacent to 11 carcinomas and had an endocrine cell population similar to that of the tumors. Endocrine cells were demonstrated in 18 (70%) of the 25 mucinous cystadenocarcinomas of the pancreas by the immunoperoxidase method although only 9 had argyrophil and argentaffin cells. The population of endocrine cells in these mucinous pancreatic tumors was similar to that found in gallbladder carcinomas. Endocrine cells were more numerous in areas with colonic-type glands, goblet cells and Paneth cells. The secretory products of the endocrine cells in these gallbladder and pancreatic tumors did not give rise to systemic endocrine manifestations. The presence of endocrine cells in these tumors can be explained on the basis of intestinal differentiation

Carcinoid tumors of the extrahepatic bile ducts: a study of seven cases

The authors report seven patients with carcinoid tumors of the extrahepatic bile ducts (EHBDs). All patients were women, with an average age at diagnosis of 49.8 years (range, 37-67 yrs). The most common presenting symptom was painless jaundice with or without pruritus. Although one patient had peptic ulcer disease before the onset of obstructive jaundice, none had systemic endocrine manifestations. These neoplasms were most often located in the common bile duct. Grossly, the carcinoid tumors were usually nodular and poorly demarcated, and ranged from 1.1 to 2.7 cm in size. Only one of the neoplasms was polypoid. Microscopically, the tumors had a trabecular or nesting pattern with occasional tubule formation, and were composed of relatively small cells with granular chromatin. All of the neoplasms expressed chromogranin and two expressed synaptophysin. Three expressed serotonin and two of the three were also immunoreactive for pancreatic polypeptide or somatostatin. Two tumors were focally positive for gastrin and one of these two tumors was also positive for serotonin and pancreatic polypeptide. All seven carcinoid tumors showed no immunoreactivity for p53, and assays for p53 loss of heterozygosity analysis were negative in two, suggesting that p53 mutations do not play a role in the pathogenesis of EHBD carcinoids. A mutation in codon 12 of K-ras was found in one carcinoid tumor whereas two of two showed immunoreactivity for Dpc4 protein. In view of the small number of carcinoids studied, the importance of these findings in the pathogenesis of these tumors is unclear. Ultrastructural examination of three of the tumors revealed numerous membrane-bound, round neurosecretory granules. Clinically, these lesions had an indolent course. Even in the presence of lymph node metastases (noted in two patients), all of the patients remained disease free 2 to 11 years (average follow up, 6.6 yrs) after segmental resection or pancreaticoduodenectomy (Whipple's procedure). Because carcinoid tumors of the EHBD are of low malignant potential, they should be separated from the more common adenocarcinomas in this locatio