Project description:In 2011, a leaf blight disease was observed on cosmos (Cosmos bipinnatus) leaves in Nonsan, Korea. The causal pathogen was isolated and identified based on morphological and molecular approaches. Morphological characteristics of the pathogen matched well with the Alternaria cosmosa and also easily distinguishable from Alternaria zinniae reported from cosmos seeds by producing branched beak. Phylogenetically, the pathogen could not be distinguished from A. passiflorae based on the sequence analysis of a combined data set of Alt a1 and gpd genes. However, A. passiflorae was distinguished from the present species by having conidiophores with 4 to 5 conidiogenous loci. The results indicate that the present Alternaria species is A. cosmosa. Pathogenicity tests revealed that the isolate was pathogenic to the leaves of Cosmos bipinnatus. This is the first report of Alternaria blight disease caused by A. cosmosa on cosmos in Korea.
Project description:Background:While stakeholder mapping is common in public policy, social sciences, and business management, this tool has not often been used in healthcare settings. We developed a new method of healthcare stakeholder mapping, which we call Contextual and Organizational Support Mapping of Stakeholders (COSMOS), to identify and assess key stakeholders in an implementation project. Stakeholder mapping allows the implementation team to assess and visually display all relevant stakeholders, their support for the project, and their ability to facilitate-or hinder-project implementation. Methods:The COSMOS model was developed to visualize the stakeholders involved in a hospital-based study conducted from 2013-2016. In this study, a new screen prompt and order set were embedded in the electronic health record to facilitate the identification and treatment of adult smokers admitted to the hospital. Physicians were the unit of randomization; physician behavior and tobacco quit rates among patients were followed for 1 year. Qualitative interviews with hospital administration, physicians, and information technology (IT) personnel (n=24) were conducted to identify the components and characteristics of the COSMOS. Results:The COSMOS consists of an organizational chart identifying all key stakeholders, with manipulation of colors and borders of the component boxes to indicate stakeholder support for the implementation project, and degree of criticality to its success. The COSMOS visualization informed the team's subsequent work by identifying potential impediments that might require additional attention to garner and maintain support throughout the project. In addition, the approach has proved to be a useful tool to explain these concepts to trainees in implementation science. Conclusion:The COSMOS schematic provides a visually rich means of identifying stakeholders, understanding their relationships to each other, displaying their level of support for the proposed implementation, and noting their criticality to the effort. The COSMOS can support researchers, project teams, administrators, and others engaged with implementation science-related work in healthcare, as well as other fields such as education, government, and industry.
Project description:An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.
Project description:BACKGROUND: With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a regular basis by researchers in many labs. RESULTS: We have now created a database called CoSMoS to find the occurrences and at the same time evaluate the significance of sequence motifs and amino acids encoded in the whole genome of the model organism Escherichia coli K12. We provide a precomputed set of multiple sequence alignments for each individual E. coli protein with all of its homologues in the RefSeq database. The alignments themselves, information about the occurrence of sequence motifs together with information on the conservation of each of the more than 1.3 million amino acids encoded in the E. coli genome can be accessed via the web interface of CoSMoS. CONCLUSION: CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in E. coli proteins.
Project description:To prolong their vase life, cut flowers are commonly kept in holding solutions. These must include a biocide to retard bacterial growth. In this study, the effect of nanosilver (NS) on certain aspects of senescence in cut garden cosmos (Cosmos bipinnatus) flowers was compared to that of the commonly used 8-hydroxyquinoline citrate (8-HQC). In combination with sucrose, both biocides prolonged cosmos vase life but did not prevent the occurrence of stem blockages. NS was more effective in limiting a reduction in endogenous soluble carbohydrates. The malondialdehyde (MDA) contents increased in senescing ray florets, both in intact and control cut flowers held in water. Both biocides were comparably effective in limiting this effect. The hydrogen peroxide content tripled in intact flowers but dropped in flowers held in water or the 8-HQC solutions; in flowers kept in NS solutions its increase was moderate. Also, the catalase activity increased in intact flowers but dropped in all cut flowers. Both biocides had similar effects on the enzyme activity, in both pure solutions and with sucrose. Most of these parameters were not significantly correlated with vase life. Overall, the effect of nanosilver on senescence in cut cosmos flowers was similar to that of 8-HQC.
Project description:LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) homologous genes have been reported to play key roles in promoting the initiation of floral meristems in raceme- and cyme-type plants. Asteraceae, a large family of plants with more than 23,000 species, has a unique head-like inflorescence termed capitulum. Here, we report a floral defective plant of the garden cosmos named green head (gh), which shows homogeneous inflorescence, indistinguishable inflorescence periphery and center, and the replacement of flower meristems by indeterminate inflorescence meristems, coupled with iterative production of bract-like organs and higher order of inflorescences. A comparison of the LFY- and UFO-like genes (CbFLY and CbUFO) isolated from both the wild-type and gh cosmos revealed that CbUFO may play an important role in inflorescence differentiation into different structures and promotion of flower initiation, and the reduced expression of CbUFO in the gh cosmos could be associated with the phenotypes of the flower-defective plants. Further expression analysis indicated that CbUFO may promote the conversion of inflorescence meristem into floral meristem in early ray flower formation, but does not play a role in its later growth period.
Project description:Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services.Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://email@example.com or firstname.lastname@example.org.Supplementary data are available at Bioinformatics online.