722 research outputs found
Rezension zu: Nico Stehr, Dustin Voss: Geld - eine Gesellschaftstheorie der Moderne
No full textRezension zu: Stehr, Nico; Voss, Dustin: Geld. Eine Gesellschaftstheorie der Moderne. Weilerswist: Velbrück Wissenschaft. 2019 ISBN 978-3-95832-166-
Pollen limitation and inbreeding depression in an ‘old rare’ bumblebee-pollinated grassland herb
No full textHabitat fragmentation and reduction of population size have been found to negatively affect plant reproduction in 'new rare' species that were formerly common. This has been attributed primarily to effects of increased inbreeding but also to pollen limitation. In contrast, little is known about the reproduction of 'old rare' species that are naturally restricted to small and isolated habitats and thus may have developed strategies to cope with long-term isolation and small population size. Here we study the effects of pollen source and quantity on reproduction of the 'old rare' bumblebee-pollinated herb, Astragalus exscapus. In two populations of this species, we tested for pollen autodeposition, inbreeding depression and outbreeding depression. Caged plants were left unpollinated or were pollinated with pollen from the same plant, from the same population or from a distant population (50 km). Additionally, we tested for pollen limitation by pollen supplementation in four populations of different size and density. In the absence of pollinators, plants did not produce seed whereas self-pollinated plants did. This indicates a self-compatible breeding system dependent on insect pollination. Both self-pollination and, in one of the two populations, cross-pollination with pollen from plants from the distant population resulted in a lower number of seeds per flower than cross-pollination with pollen from plants from the resident population, indicating inbreeding and outbreeding depression. Pollen addition enhanced fruit set and number of seeds per flower in three of the four populations, indicating pollen limitation. The degree of pollen limitation was lowest in the smallest but densest population. Our results suggest that, similar to 'new rare' plant species, also 'old rare' species may be at risk of inbreeding depression and pollen limitation.German Federal Environmental Foundation (Deutsche Bundesstiftung Umwelt
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
No full textMotivation: Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. Results: We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene regulation
Cotithene globulicollis Voss
No full textCotithene globulicollis Voss Cotithene globulicollis Voss 1940: 4 Diagnosis. Length 4.5–6.1 mm; rostrum in male (Fig. 8 A) in lateral view angulate and expanded near apical 2 / 5, slightly impressed along basal 1 / 5, head (Fig. 8 A) with small, posterior, triangular projection and sparse, longer, recurvate setae, pronotum (Fig. 1 B) expanded, light reddish-brown, prosternum with small obtuse elevation in front of each procoxal cavity, elytra dark-reddish-brown, aedeagus (Fig. 11) apically evenly narrowed, internal sac without ventral, annulate structure; female with color pattern as that of male, procoxal cavities separated by about width of antennal club, spermatheca (Fig. 11) constricted near apical 3 / 5; association with Asplundia Harling. Cotithene globulicollis may be distinguished from similarly sized members of the leptorhamphis-trigaea clade by the particular combination of modifications on the head and prosternum in males, and by the shorter and wider rostrum in females. This species furthermore differs from members of the anaphalanta-melanoptera clade by its color pattern and characteristics of the male and female terminalia. Description. Male. Length 5.5–6.1 mm, width 2.4–2.8 mm, l/w = 2.2 (N = 3). Color light reddish-brown, rostrum and head slightly darker, legs yellowish-brown, elytra darker, brown. Rostrum (Fig. 8 A) 1.5–1.7 mm, r/p = 0.6–0.8; dorsally slightly arcuate, angulate and tumescent near apical 2 / 5, ventrally straight; dorsally slightly impressed along basal 1 / 5 (cf. Voss 1940: 5, "muldenartig vertieft"); antennal insertion at apical 1 / 3 to 2 / 5. Head (Fig. 8 A) with slight transverse elevation extending between posterodorsal edges of eyes, with small, posterior, triangular projection, setation sparse, short, recurvate; area adjacent to posterior margin of eye strongly projected, dorsally with row of short, recurvate setae. Pronotum (Fig. 1 B) expanded (with apparent positive allometry), anterolaterally shallowly impressed. Prosternum with anterior margin tumescent, projected anteroventrad, anterior half transversely impressed, thereafter with shallow impression, anterolaterally of each procoxal cavity with obtuse tumescence; procoxal cavities separated by slightly more than width of antennal club. Legs light reddish-brown to yellow. Scutellum largely covered by elytra. Elytra (Fig. 1 B) posteriorly slightly attenuate, widest at humeri, gradually narrowing in posterior two-thirds; slightly convex, anterior elevation present, extending along basal 1 / 5 of I–V; striae slightly narrower than intervals, VIII–X deeper. Spiculum gastrale shorter than aedeagus; furcal arms slightly arcuate, apically narrowed. Adeagus (Fig. 11) l/ w = 3.1–3.3 (N = 3), widest near middle, strongly narrowing in apical 1 / 5, apex rounded, medially slightly projected; in lateral view apically gradually narrowed, dorsal and ventral margins straight; internally with a symmetrical, narrowly V-shaped pair of explanate sclerites; sclerites in lateral view triangular, slightly deflexed, margins undulate; apodemes shorter than body. Female. Length 4.5–5.9 mm, width 2.1–2.6 mm, l/w = 2.1–2.3 (N = 3). Color more homogeneously reddish-brown than in male. Rostrum (Fig. 8 B) 1.6–1.9 mm, r/p = 0.9 –1.0; narrow, width similar throughout; antennal insertion at apical 2 / 5 to middle region. Pronotum less expanded. Prosternum without anterior impressions or tumescences; procoxal cavities separated by about width of antennal club. Elytra posteriorly rounded, widest near anterior third; anterior elevation less distinct; striae shallower than in male. Sternum VIII (Fig. 11) with furcal arms slightly arcuate, subparallel, apices with 4–6 setae. Spermatheca (Fig. 11) C-shaped, inner and outer margins constricted near apical 3 / 5, apex triangular, acuminate, deflected. Material examined. Male syntype "coll. DEI Eberswalde / Cotithene globulicollis nv. / Syntypus [red label] / Cotithene globulicollis m. [green label] / Voss det. / Costa Rica, Turrialba, VI, 900 m [green label] /?" (DEIC). Other specimens: " Costa Rica, Limón, P.N. Br. Carillo, Q. González, 50 m, N 10 °09' 78 '', W 83 ° 56 ' 17 '', on Asplundia sp. inflor., leg. N. Franz, VI- 11-2003 " (DEIC, 1 male); " Costa Rica, P. Her. [Heredia], Est. Biol. La Selva (OTS), 40 m, 27 -IV- 1997, # 3, leg. N. Franz" (CWOB, 1 male); " Costa Rica, Heredia, La Selva, 40 m, on Asplundia vagans, leg. N. Franz, IV- 10-1999 " (NMFC, 1 male); " Costa Rica, Alaj. [Alajuela], Est. Biol. San Ramon, xi– xii- 1999, 900 m, P. Hanson, malaise trap" (CWOB, 1 male); " Costa Rica, Limón, P.N. Br. Carillo, Q. González, 50 m, N 10 °09' 78 '', W 83 ° 56 ' 17 '', on Asplundia sp. inflor., leg. N. Franz, VI- 11-2003 " (DEIC, 1 female; NMFC, 1 female); " Costa Rica: Alajuela, E.B. San Ramon, R.B. San Ramon, 27 km N & 8 km W San Ramon, 10 ° 13 ' 30 '' N, 84 ° 35 ' 30 '' W, 850–950 m, 29.VI- 6.VII. 1999, R. Anderson, wet premontane forest, 99-108 / on Asplundia vagans flowers" (CMNC, 1 female); " Costa Rica: Alajuela, Los Lagos, Volcan Arenal, 600 m, 10 ° 29 ' N, 84 ° 43 ' 30 '' W, 26.III. 2000, R. Anderson, on Asplundia (epiphytic)" (CMNC, 1 female); " Panama, Bocas del Toro, Corriente Grande, Rio Changuinola/ 9 ° 17 ' 30 N, 82 ° 32 ' 41 '' W, H. Wolda/ II- 7-1980 " (CWOB, 1 female). Natural history. Cotithene globulicollis occurs at various localities in the Costa Rican Cordillera Central (Fig. 13 A), including La Selva (OTS), Quebrada González (Braulio Carrillo), San Ramón (UCR), Turrialba (type locality) and Volcán Arenal, as well as on the Atlantic slope of Panama, Río Changuinola (Bocas del Toro). The reported host associations are with several species of Asplundia Harling, in addition to Asplundia vagans Harling as recorded. At La Selva, Costa Rica, 4–6 individuals were taken on inflorescences of Asplundia euryspatha and A. vagans (Franz 2007 b). Typically only 1– 2 adults occur on an inflorescence, and their arrival and departure periods are not well synchronized with the anthesis of the inflorescence. Some individuals collected carried small quantities of pollen on different parts of their body. However, their low abundance, the absence of synchronized patterns of arrival and departure and their relatively large size preclude regular contacts with the plant's female flowers during receptivity. Therefore, C. globulicollis weevils are not pollinators of their hosts. Indeed, their behavior on the inflorescences is fairly destructive, as they feed on various floral parts including unopened anthers, bases of the male flowers and all structures of the female flowers. Following arrival, the females of C. globulicollis locate a suitable position on the surface of the inflorescence and then chew their way towards the central axis, into which they eventually oviposit. An entry hole is left after this activity. A single larva hatches and develops inside by feeding along the central axis and adjacent pulp and seeds, which may ultimately cause abortion of the infructescence. Large larvae were located in aborted infructescences, indicating that C. globulicollis larvae can consume living as well as rotting plant tissue during the final stages of development. Their destructive behavior has convergent similarities with Systenotelus Anderson & Gómez, a non-pollinating seed predator of Panama-hat palms in the genus Carludovica Ruíz & Pavón (Franz 2004).Published as part of Franz, Nico M., 2008, Revision, phylogeny and natural history of Cotithene Vo s s (Coleoptera: Curculionidae), pp. 1-33 in Zootaxa 1782 on pages 21-24, DOI: 10.5281/zenodo.18235
Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
No full textAbstract Background Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function. Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments. Results We developed a novel approach to find key transcription factors that may explain concerted expression changes of specific components of the signal transduction network. The approach aims at revealing evidence of positive feedback loops in the signal transduction circuits through activation of pathway-specific transcription factors. We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways. Application of the approach to the microarray gene expression data on TNF-alpha stimulated primary human endothelial cells helped to reveal novel key transcription factors potentially involved in the regulation of the signal transduction pathways of the cells. Conclusion We developed a novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC® and TRANSPATH®). The corresponding software and databases are available at http://www.gene-regulation.com.</p
Molecular mechanistic associations of human diseases
No full textBackground: The study of relationships between human diseases provides new possibilities for biomedical research. Recent achievements on human genetic diseases have stimulated interest to derive methods to identify disease associations in order to gain further insight into the network of human diseases and to predict disease genes. Results: Using about 10000 manually collected causal disease/gene associations, we developed a statistical approach to infer meaningful associations between human morbidities. The derived method clustered cardiometabolic and endocrine disorders, immune system-related diseases, solid tissue neoplasms and neurodegenerative pathologies into prominent disease groups. Analysis of biological functions confirmed characteristic features of corresponding disease clusters. Inference of disease associations was further employed as a starting point for prediction of disease genes. Efforts were made to underpin the validity of results by relevant literature evidence. Interestingly, many inferred disease relationships correspond to known clinical associations and comorbidities, and several predicted disease genes were subjects of therapeutic target research. Conclusions: Causal molecular mechanisms present a unifying principle to derive methods for disease classification, analysis of clinical disorder associations, and prediction of disease genes. According to the definition of causal disease genes applied in this study, these results are not restricted to genetic disease/gene relationships. This may be particularly useful for the study of long-term or chronic illnesses, where pathological derangement due to environmental or as part of sequel conditions is of importance and may not be fully explained by genetic background.European Union [LSHM-CT-2006-518153, 200754
Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer.
No full textThe molecular causes by which the epidermal growth factor receptor tyrosine kinase induces malignant transformation are largely unknown. To better understand EGFs' transforming capacity whole genome scans were applied to a transgenic mouse model of liver cancer and subjected to advanced methods of computational analysis to construct de novo gene regulatory networks based on a combination of sequence analysis and entrained graph-topological algorithms. Here we identified transcription factors, processes, key nodes and molecules to connect as yet unknown interacting partners at the level of protein-DNA interaction. Many of those could be confirmed by electromobility band shift assay at recognition sites of gene specific promoters and by western blotting of nuclear proteins. A novel cellular regulatory circuitry could therefore be proposed that connects cell cycle regulated genes with components of the EGF signaling pathway. Promoter analysis of differentially expressed genes suggested the majority of regulated transcription factors to display specificity to either the pre-tumor or the tumor state. Subsequent search for signal transduction key nodes upstream of the identified transcription factors and their targets suggested the insulin-like growth factor pathway to render the tumor cells independent of EGF receptor activity. Notably, expression of IGF2 in addition to many components of this pathway was highly upregulated in tumors. Together, we propose a switch in autocrine signaling to foster tumor growth that was initially triggered by EGF and demonstrate the knowledge gain form promoter analysis combined with upstream key node identification
H. Douglas Goff and Karen Voss Peters with their plaques
No full textpermission received.H. Douglas Goff with the plaque he received for the book he authored, "Ice Cream", and Karen Voss Peters with the plaque she received for the book she author, "William meets the Stick family " at the Campus Author Recognition Program annual reception, November 7, 2013.http://author.lib.uoguelph.ca/viewAuthorBook.cfm?biblioId=605 and http://author.lib.uoguelph.ca/viewAuthorBook.cfm?biblioId=630The University of Guelph Librar
ExPlain (TM): finding upstream drug targets in disease gene regulatory networks
No full textDifferent signal transduction pathways leading to the activation of transcription factors (TFs) converge at key molecules that master the regulation of many cellular processes. Such crossroads of signalling networks often appear as Achilles Heels causing a disease when not functioning properly. Novel computational tools are needed for analysis of the gene expression data in the context of signal transduction and gene regulatory pathways and for identification of the key nodes in the networks. An integrated computational system, ExPlain (TM) (www.biobase.de) was developed for causal interpretation of gene expression data and identification of key signalling molecules. The system utilizes data from two databases (TRANSFAC (R) and TRANSPATH (R)) and integrates two programs: (1) Composite Module Analyst (CMA) analyses 5'-upstream regions of co-expressed genes and applies a genetic algorithm to reveal composite modules (CMs) consisting of co-occurring single TF binding sites and composite elements; (2) ArrayAnalyzer (TM) is a fast network search engine that analyses signal transduction networks controlling the activities of the corresponding TFs and seeks key molecules responsible for the observed concerted gene activation. ExPlain (TM) system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation
Analysis of the regulatory network of APP, amyloid beta protein precursor, with the signal transcluction database TRANSPATH (R) Professional
No full text- …
