783 research outputs found
Hormone Signaling Networks Open Multiple Routes for Immunity and Disease in Plants
No full textPlant hormones are small signaling molecules that regulate almost every aspect of plant life cycle. Plant pathogens alter hormonal balance of the host to cause disease. In response, host redefines hormone signaling networks to cope with the invading pathogen. Biotrophic pathogens are generally sensitive to salicylic acid mediated defense responses, whereas necrotrophic pathogens are deterred through jasmonate/ethylene pathways. Interaction between these pathways is regarded as central backbone of plant immunity. Classic hormones such as auxin, gibberellin, and cytokinin either promote salicylic acid or jasmonates mediated networks of immunity in plants. Here, we advocate a network biology perspective and emphasize the application of systems biology approaches for a comprehensive understanding of plantpathogen interactions.Review | Biohelikon: Immunity and Diseases
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
No full textMüller T, Rahmann S, Dandekar T, Wolf M. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology. 2004;4(1): 20.Background: In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Results: Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ) then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Conclusions: Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap
XML schemas for common bioinformatic data types and their application in workflow systems
No full textSeibel PN, Krüger J, Hartmeier S, et al. XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics. 2006;7(1): 490.Background: Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results: Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. Conclusion: The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios
IoWoman, March/April 2004, Vol.34, no.2
No full textNewsletter for the Iowa Commission on the Status of Wome
IoWoman, March/April 2004, Vol. 34, no. 2
No full textNewsletter for the Iowa Commission on the Status of Wome
Modulating the levels of plant hormone cytokinins at the host-pathogen interface
No full textCytokinins are adenine and non-adenine derived heterogeneous class of regulatory molecules that participate in almost every aspect of plant biology. They also affect plant defense responses as well as help microbial pathogens to establish pathogenesis. The functional approaches that ensure desired and subtle modulations in the levels of plant cytokinins are highly instrumental in assessing their functions in plant immunity. Here, we describe a detailed working protocol regarding the enhanced production of cytokinins from plants that harbor isopentenyltransferase (IPT) enzyme gene under the control of 4xJERE (jasmonic acid and elicitor-responsive element) pathogen-inducible promoter. Our devised expression system is a context-dependent solution when it comes to investigating host-pathogen interactions under the modulated conditions of plant cytokinins.</p
Paramacrobiotus kenianus Schill, Forster, Dandekar & Wolf 2010
No full text157. Paramacrobiotus kenianus Schill, Förster, Dandekar & Wolf, 2010 [T] MacRobiotus ‘RichteRsi gRoups’ 1 and 2 (Hengherr et al. 2008, 2009a) MacRobiotus ‘RichteRsi gRoups’ 2 and 1 (Hengherr et al. 2009b) MacRobiotus ‘RichteRsi gRoups’ 2 and 3 (Guidetti et al. 2009) PaRamacRobiotus kenianus sp. nov. (Schill et al. 2010) Terra typica: Kenya (Africa) Kenya: • 00°18′S; 36°05′E; 1,800 m asl: Type Locality: Nakuru County, Nakuru, moss. Hengherr et al. (2008, 2009a, b), Guidetti et al. (2009), Schill et al. (2010) • 00°43′S; 36°26′E; 1,900 m asl: Nakuru County, Naivasha, moss. Hengherr et al. (2008, 2009a, b), Guidetti et al. (2009), Schill et al. (2010) Record numbers. Kenya: 2; total: 2. Remarks. This species, identified only via DNA barcoding and biophysical data, is morphologically identical to P. richtersi (Guidetti et al. 2009, Schill et al. 2010). The International Commission of the Zoological Nomenclature code states, “An author, when drawing up the description of a new nominal taxon, should include comparisons with appropriate related taxa in order to assist later identification of the taxon. Namebearing type material should be illustrated (or a reference given to such illustration).” (http://www.nhm.ac.uk/ hosted-sites/iczn/code/index.jsp?nfv=true&booksection=appendixB). This taxon, in the absence of such illustration, remains a cryptic species identifiable only via DNA and biophysical data. Currently endemic to Kenya.Published as part of Kaczmarek, Łukasz, 2017, Annotated zoogeography of non-marine Tardigrada. Part IV: Africa, pp. 1-74 in Zootaxa 4284 (1) on page 55, DOI: 10.11646/zootaxa.4284.1.1, http://zenodo.org/record/101040
Diagnostic value of preoperative CT scan to stratify colon cancer for neoadjuvant therapy
No full textNeoadjuvant therapy could improve oncological outcome of patients suffering from colon cancer. An accurate staging method is needed to define suitable patients. The aim of this retrospective study was to validate the value of CT for identifying patients with local advanced (T3/4) or nodal-positive colon cancer. Preoperative abdominal CT scans of 210 patients with colon cancer were evaluated by two radiologists independently for the T stage and N stage. Results were compared to pathology. Patients were stratified according to the guidelines for rectal cancer into patients with low risk (T0/1/2 and N0) or high risk (T3/4 or N+). Inter-observer correlation was high with over 90 %. Overall sensitivity T stage was 93.0 % and for N stage 76.9 %. Using CT scan to identify local advanced (T3/4 or N+) tumors, the consensus sensitivity was 94.9 %, the specificity 53.6 %, the positive predictive value (PPV) 92.8 %, and the negative predictive value (NPV) 62.5 %. Computer tomography represents an effective tool for identifying patients with colon cancer suitable for neoadjuvant therapy according to the guidelines for rectal cancer.German Research Foundation (DFG); University of Wurzbur
Gene expression profiles and protein–protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia
No full textSergey Shityakov,1 Thomas Dandekar,2 Carola Förster1 1Department of Anesthesia and Critical Care, 2Department of Bioinformatics, University of Würzburg, Würzburg, Germany Abstract: Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) between the samples from AIDS patients with and without apparent features of HIVE-induced dementia were identified. In addition, protein–protein interaction networks were constructed by mapping DEGs into protein–protein interaction data to identify the pathways that these DEGs are involved in. The results revealed that the expression of 1,528 DEGs is mainly involved in the immune response, regulation of cell proliferation, cellular response to inflammation, signal transduction, and viral replication cycle. Heat-shock protein alpha, class A member 1 (HSP90AA1), and fibronectin 1 were detected as hub nodes with degree values >130. In conclusion, the results indicate that HSP90A and fibronectin 1 play important roles in HIVE pathogenesis.Keywords: microarray, human immunodeficiency virus, differentially expressed genes, protein–protein interaction network, gene ontology, encephalitis, dementi
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