G84-702 Root and Soil Analayses for Nematodes in Corn

This NebGuide describes how to interpret laboratory results of samples submitted for nematode analysis and discusses ten species that are potentially damaging to corn. Several kinds of plant parasitic nematodes (small, soil-inhabiting roundworms) are associated with root injury, poor plant color, stunted growth, and reduced grain yields in field corn. Symptoms caused by these pests are often confused with root rot diseases, nutritional deficiencies or climatic stresses. Special laboratory analyses are, therefore, necessary to determine if nematodes are the primary cause of reduced corn performance. Since corn growers may be unfamiliar with nematode diseases, the following discussion of laboratory reports may be helpful

Distribution of Soybean Cyst Nematode in Nebraska

A survey of 552 soybean fields in 20 counties in Nebraska in 1986-88 revealed 35 fields infested with the soybean cyst nematode (SCN), Heterodera glycines. Identification was confirmed with a greenhouse bioassay, using \u27Lee 74\u27 soybean, and by the application of a DNA hybridization probe derived from SCN mitochondrial DNA. Most of the SCN-infested fields were located on the Missouri River floodplain and in the southeastern corner of the state

Popcorn : production and marketing

"K. E. Ziegler, Iowa State University; R. B. Ashman, Purdue University; G. M. White, University of Kentucky; and D. S. Wysong, University of Nebraska ; Reviewers: M. A. Hanna, University of Nebraska Seed Research Committee, Popcorn Institute, IL R. L. Nielsen, Purdue University M. S. Zuber, University of Missouri."--First page.K. E. Ziegler (Iowa State University), R. B. Ashman (Purdue University), G. M. White (University of Kentucky), and D. S. Wysong (University of Nebraska), M. A. Hanna (University of Nebraska Seed Research Committee, Popcorn Institute, IL), R. L. Nielsen (Purdue University), M. S. Zuber (University of Missouri)New 2/85/5

Popcorn production and marketing

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311

Data submission and curation for caArray, a standard based microarray data repository system

caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG™), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG™. 

Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the MAGE-TAB, a spreadsheet-based format for annotating and communicating microarray data in a MIAME-compliant fashion ("http://www.mged.org/mage-tab":http://www.mged.org/mage-tab). MAGE-TAB is built on community standards – MAGE, MIAME, and Ontology. The components and work flow of MAGE-TAB files are organized in such a way which is already familiar to bench scientists and thus minimize the time and frustration of reorganizing their data before submission. The MAGE-TAB files are also structured to be machine readable so that they can be easily parsed into database. Users can control public access to experiment- and sample-level data and can create collaboration groups to support data exchange among a defined set of partners. 

All data submitted to caArray at NCI will go through strict curation by a group of scientists against these standards to make sure that the data are correctly annotated using proper controlled vocabulary terms and all required information are provided. Two of mostly used ontology sources are MGED ontology ("http://mged.sourceforge.net/ontologies/MGEDontology.php":http://mged.sourceforge.net/ontologies/MGEDontology.php) and NCI thesaurus ("http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do":http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). The purpose of data curation is to ensure easy comparison of results from different labs and unambiguous report of results. 

Data will also undergo automatic validation process before parsed into database, in which minimum information requirement and data consistency with the array designs are checked. Files with error found during validation are flagged with error message. Curators will re-examine those files and make necessary corrections before re-load the files. The iteration repeats until files are validated successfully. Data are then imported into the system and ready for access through the portal or through API. Interested parties are encouraged to review the installation package, documentation, and source code available from "http://caarray.nci.nih.gov":http://caarray.nci.nih.gov

Hsp90 orchestrates transcriptional regulation by Hsf1 and cell wall remodelling by MAPK signalling during thermal adaptation in a pathogenic yeast

Acknowledgments We thank Rebecca Shapiro for creating CaLC1819, CaLC1855 and CaLC1875, Gillian Milne for help with EM, Aaron Mitchell for generously providing the transposon insertion mutant library, Jesus Pla for generously providing the hog1 hst7 mutant, and Cathy Collins for technical assistance.Peer reviewedPublisher PD

Efficacy and pharmacokinetic/pharmacodynamic evaluation of the Aurora kinase A inhibitor MLN8237 against preclinical models of pediatric cancer

To gain a greater understanding of the potential of the Aurora kinase A inhibitor MLN8237 in the treatment of pediatric malignancies. The activity of MLN8237 was evaluated against 28 neuroblastoma and Ewing sarcoma cell lines, and its in vivo efficacy was studied over a range of doses against 12 pediatric tumor xenograft models. Pharmacokinetic, pharmacodynamic, and genomic studies were undertaken. In vitro neuroblastoma cell lines were generally more sensitive to MLN8237 than Ewing sarcoma lines. MLN8237 demonstrated significant activity in vivo against solid tumor models at the maximum tolerated dose (MTD); however, only 2 of 6 neuroblastoma models had objective responses at 0.25MTD. In contrast, MLN8237 induced objective responses at its MTD and at 0.5MTD in three ALL models and in two out of three at 0.25MTD. Pharmacokinetic studies at 0.5MTD demonstrated a T (max) of 0.5 h, C (max) of 24.8 mu M, AUC((0-24)) of 60.3 mu M h, and 12 h trough level of 1.2 mu M. Mitotic indices increased 6-12 h after MLN8237 administration. AURKA copy number variation was frequent in xenografts, and expression was highly correlated with copy number. Objective responses were more frequent in tumors with decreased AURKA copy number (5/8) compared to those with increased gene copy number (2/14). This report confirms the significant activity against both solid tumor and ALL xenografts at the MTD, with a steep dose response. These data support clinical development of MLN8237 in childhood cancer. Because of the steep dose-response relationship, such studies should target achieving trough levels of 1 mu M or higher for sustained periods of treatment

Validation of a 40-Gene Expression Profile Test to Predict Metastatic Risk in Localized High-Risk Cutaneous Squamous Cell Carcinoma

Background: Current staging systems for cutaneous squamous cell carcinoma (cSCC) have limited positive predictive value (PPV) for identifying patients who will experience metastasis. Objective: To develop and validate a gene expression profile (GEP) test for predicting risk for metastasis in localized, high-risk cSCC with the goal of improving risk-directed patient management. Methods: Archival formalin-fixed paraffin-embedded primary cSCC tissue and clinicopathologic data (n=586) were collected from 23 independent centers in a prospectively designed study. A GEP signature was developed using a discovery cohort (n=202) and validated in a separate, non-overlaping, independent cohort (n=324). Results: A prognostic, 40-gene expression profile (40-GEP) test was developed and validated, stratifying high-risk cSCC patients into classes based on metastasis risk: Class 1 (low-risk), Class 2A (high-risk), and Class 2B (highest-risk). For the validation cohort, 3-year metastasis-free survival (MFS) rates were 91.4%, 80.6%, and 44.0%, respectively. A PPV of 60% was achieved for the highest-risk group (Class 2B), an improvement over staging systems; while negative predictive value, sensitivity, and specificity were comparable to staging systems. Limitations: Potential understaging of cases could affect metastasis rate accuracy.Conclusion: The 40-GEP test is an independent predictor of metastatic risk that can complement current staging systems for patients with high-risk cSCC