Plant Transcription Factors @ uni-potsdam.de

We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae _Chlamydomonas reinhardtii_, _Ostreococcus tauri_ and the vascular plants _Oryza sativa_ and _Arabidopsis thaliana_

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors

<p>Abstract</p> <p>Background</p> <p>Quantitative reverse transcription – polymerase chain reaction (qRT-PCR) has been demonstrated to be particularly suitable for the analysis of weakly expressed genes, such as those encoding transcription factors. Rice (<it>Oryza sativa </it>L.) is an important crop and the most advanced model for monocotyledonous species; its nuclear genome has been sequenced and molecular tools are being developed for functional analyses. However, high-throughput methods for rice research are still limited and a large-scale qRT-PCR platform for gene expression analyses has not been reported.</p> <p>Results</p> <p>We established a qRT-PCR platform enabling the multi-parallel determination of the expression levels of more than 2500 rice transcription factor genes. Additionally, using different rice cultivars, tissues and physiological conditions, we evaluated the expression stability of seven reference genes. We demonstrate this resource allows specific and reliable detection of the expression of transcription factor genes in rice.</p> <p>Conclusion</p> <p>Multi-parallel qRT-PCR allows the versatile and sensitive transcriptome profiling of large numbers of rice transcription factor genes. The new platform complements existing microarray-based expression profiling techniques, by allowing the analysis of lowly expressed transcription factor genes to determine their involvement in developmental or physiological processes. We expect that this resource will be of broad utility to the scientific community in the further development of rice as an important model for plant science.</p

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors

<p>Abstract</p> <p>Background</p> <p>Quantitative reverse transcription – polymerase chain reaction (qRT-PCR) has been demonstrated to be particularly suitable for the analysis of weakly expressed genes, such as those encoding transcription factors. Rice (<it>Oryza sativa </it>L.) is an important crop and the most advanced model for monocotyledonous species; its nuclear genome has been sequenced and molecular tools are being developed for functional analyses. However, high-throughput methods for rice research are still limited and a large-scale qRT-PCR platform for gene expression analyses has not been reported.</p> <p>Results</p> <p>We established a qRT-PCR platform enabling the multi-parallel determination of the expression levels of more than 2500 rice transcription factor genes. Additionally, using different rice cultivars, tissues and physiological conditions, we evaluated the expression stability of seven reference genes. We demonstrate this resource allows specific and reliable detection of the expression of transcription factor genes in rice.</p> <p>Conclusion</p> <p>Multi-parallel qRT-PCR allows the versatile and sensitive transcriptome profiling of large numbers of rice transcription factor genes. The new platform complements existing microarray-based expression profiling techniques, by allowing the analysis of lowly expressed transcription factor genes to determine their involvement in developmental or physiological processes. We expect that this resource will be of broad utility to the scientific community in the further development of rice as an important model for plant science.</p

PlnTFDB: an integrative plant transcription factor database

BACKGROUND: Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. DESCRIPTION: PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family. CONCLUSION: We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through . Further data will be included in the future when the sequences of other plant genomes become available

Istraživanje novog tehničko-tehnološkog rešenja u zasnivanju voćnjaka kombinovanim oruđem rigoler –razrivač u obradi zemljišta

Modern agriculture requires the use of modern technology, with new technical and technological solutions. Basic agro-technical operation in phase of establishing orchards and vineyards that requires large amounts of energy is plowing, for its specificity called rigoling. Trenching phase consumes greatest portion of energy int he processing and preparation of land in general and especially for the establishment of cultural agricultural fruit-grape production. There are more operational technologies, and this paper analyses classical technology, and combined technology using rigoler and plowing tools for soil cultivation. When classic technologies are applied, soil is cut and sectioned, moved and crushed, thus creating loose soil layer. The depth of processed soil is different for different fruitgrape crops, depending on the needs of the root system, as penetration depth and the breadth of development, ranging between 60 and 100 cm. Such technology moves active soil layer to the inactive bottom of the furrow, while inactive soil layer is removed to the surface. This technology has to be defined for different soil types. Combined technical-technological solution using a rigoler with built-in plow enables the achievement of working depth required by the root system, but the inactive soil layer is not moved to the surface of the plowed soil. The lower topsoil layer is only shaken and broken. Work technology combining rigoler and plow in one pass, can significantly increase technological production, while saving significant amounts of energy. This technology should be applied to avoid unnecessary expenditure of energy.U radu su prikazani rezultati ostvarenih vučnih otpora pri rigolovanju zemljišta sa plugom rigolerom na dubini od 60 cm, 70 cm, 80 cm i 90 cm, kao i vučni otpori rigolera sa dodatnim radnim organom u obliku dleta. Dodatkom dleta, dubina rigolovanja po varijantama rada, povećana je za 10 cm, 15 cm i 20 cm. Dobijeni rezultati pokazuju da na povećanim dubinama rigolovanja, specifičan otpor zemljišta ima nepromenjenu vrednost kao i pri samom rigolovanju. Ovo se postiže time što je odnos povećane dubine rigolovanja veći od povećanog vučnog otpora sa dodatkom dleta. Ekonomičnost upotrebe dleta je do 70 cm rigolovanja i 20 cm dubine rada dleta. Iznad 70 cm rigolovanja primena dleta se ekonomski smanjuje, jer se na toj dubini ispunjava agrotehnički zahtev

Suzbijanje zelene vaši jabuke (Aphis pomi De Geer) u organskoj proizvodnji

The efficacy of different methods for controlling populations of green apple aphid (Aphis pomi De Geer) in organic apple orchard was compared over three consecutive years. The following three control methods were tested: a) predator activity (Coccinela septempunctata), b) predator activity (C. septempunctata) + selective spraying of trees with infestation level exceeding 10% with a botanical insecticide (NeemAzal T/S), and c) predator activity (C. septempunctata) + total spraying of all orchard trees with the botanical insecticide (NeemAzal T/S). In terms of maintaining a biological balance within an orchard, the combination of natural regulation by C. septempunctata and selective spraying of individual trees with NeemAzal T/S proved to be the most efficient method.Upoređivana je efikasnost različitih metoda suzbijanja populacija zelene vaši jabuke (Aphis pomi De Geer) u organskom zasadu jabuka tokom tri godine. Ispitane su tri metode suzbijanja: a) aktivnost predatora (Coccinela septempunctata), b) aktivnost predatora (C. septempunctata) + selektovno prskanje stabala sa preko 10% zaraženosti botaničkim insekticidom (NeemAzal T/S) i c) aktivnost predatora (C. septempunctata) + prskanje svih stabala u voćnjaku botaničkim insekticidom (NeemAzal T/S). Sa stanovišta održavanja biološke ravnoteže u voćnjaku, najefikasniji metod predstavljala je kombinacija prirodne regulacije putem vrste C. septempunctata i selektivnog prskanja pojedinačnih stabala preparatom NeemAzal T/S

Control of green apple aphid (Aphis pomi De Geer) in organic apple production

The efficacy of different methods for controlling populations of green apple aphid (Aphis pomi De Geer) in organic apple orchard was compared over three consecutive years. The following three control methods were tested: a) predator activity (Coccinela septempunctata), b) predator activity (C. septempunctata) + selective spraying of trees with infestation level exceeding 10% with a botanical insecticide (NeemAzal T/S), and c) predator activity (C. septempunctata) + total spraying of all orchard trees with the botanical insecticide (NeemAzal T/S). In terms of maintaining a biological balance within an orchard, the combination of natural regulation by C. septempunctata and selective spraying of individual trees with NeemAzal T/S proved to be the most efficient method

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors-0

<p><b>Copyright information:</b></p><p>Taken from "A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors"</p><p>http://www.plantmethods.com/content/3/1/7</p><p>Plant Methods 2007;3():7-7.</p><p>Published online 8 Jun 2007</p><p>PMCID:PMC1914063.</p><p></p>DNA (gDNA), evaluation of cDNA quality, primer design and data analysis. The absence of gDNA was confirmed by quantitative RT-PCR (qRT-PCR) with primer pairs targeting various non-coding regions. The quality of the cDNA was tested using different reference genes, as outlined in the text

A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors-1

<p><b>Copyright information:</b></p><p>Taken from "A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors"</p><p>http://www.plantmethods.com/content/3/1/7</p><p>Plant Methods 2007;3():7-7.</p><p>Published online 8 Jun 2007</p><p>PMCID:PMC1914063.</p><p></p>erent at p = 0.001. Non-parametric comparison of mean values (Mann-Whitney U test) confirmed the presence of statistically significant differences at p = 0.000001. Transformation to expression values revealed that the slightly different PCR efficiencies could lead to a mean difference of maximal 0.3, when the fold change was expressed as log. Individual primer pairs can thus exhibit slight differences for their target genes in different cultivars. However, this does not significantly affect the overall applicability of the primer platform for expression profiling experiments (Caldana ., manuscript in preparation)