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Plant Transcription Factors @ uni-potsdam.de Nature Precedings
Diego Mauricio Riaño-Pachón; Ingo Dreyer; Slobodan Ruzicic; Bernd Mueller-Roeber.
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_.
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/243/version/1
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Reversal of an immunity associated plant cell death program by the growth regulator auxin Nature Precedings
Suresh Gopalan.
One form of plant immunity against pathogens involves a rapid host programmed cell death at the site of infection accompanied by resistance, termed the hypersensitive response (HR). Here it is shown that the HR programmed cell death program initiated by the bacterial type III secretion system dependent proteinaceous elicitor harpin from Erwinia amylovora can be reversed till very late in the process by the plant growth regulator auxin. Early inhibition or late reversal of this cell death program does not affect marker genes tightly correlated with local and systemic resistance. Cross-regulation between cell death programs and growth regulators is prevalent in different kingdoms. Thus, the concept that cell death program can be reversed till late provides a...
Tipo: Manuscript Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1347/version/1
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CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer arietinum L) Nature Precedings
Manoj D. R. Rajput; Kailash C. Upadhyaya.
We report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (_Cicer arietinum_ retro-element 1) in chickpea. This 5920-bp AT-rich (63%) element carries 723-bp 5' and 897-bp 3' LTRs respectively flanking an internal region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5' LTR and a 13-bp polypurine tract upstream to 3' LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy group of retrotransposons....
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/819/version/1
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Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence Nature Precedings
Xiaohan Yang; Gerald A. Tuskan; Timothy J. Tschaplinski; (Max) Zong-Ming Cheng.
Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/320/version/1
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Plant Functional Types and Plant Trait Measurements in the Eastern Ghats, South India Nature Precedings
K. Anupama; A. Stephen; S. Aravajy; G. Orukaimani.
Classifying terrestrial plant species on the basis of function rather than on taxonomy facilitates addressing ecological questions at the scale of ecosystems, landscapes or Biomes. The concept of plant functional types (PFTs) helps handle taxonomic diversity, as it groups together species that share common attributes with respect to, e.g. life-form, phenology and bioclimatic limits. For some time now, large international efforts promoted by the IGBP-GCTE programme are underway to measure for a large number of species a shortlist of significant plant traits that would underlie such functional plant classification systems. The idea here is to help address vegetation responses to and vegetation effects on environmental changes such as climate changes, but...
Tipo: Poster Palavras-chave: Ecology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/941/version/1
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Rapid Dissolution of Lignocellulosic Plant Materials in an Ionic Liquid Nature Precedings
Sierra Rayne; Giuseppe Mazza.
Concerns regarding the non-renewable nature of, and pollution from, petroleum derived energy and commercial products has led to the concept of a biomass economy. As part of this vision for a society based on sustainable biomaterials, proposed biorefineries need to tackle the challenges of taking a wide diversity of raw biomass and rapidly and effectively transforming it into functionalizable platform molecules that can be derivatized into industrial and consumer products, or converted into biofuels. A substantial research effort is underway focussed on degrading biomass into smaller constituents using a variety of physical, chemical, and biological processes. One promising technology for the solubilization of biomass is ionic liquids (ILs), which has...
Tipo: Manuscript Palavras-chave: Chemistry; Earth & Environment; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/637/version/1
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PlnTFDB: Plant Transcription Factor Database – Update Nature Precedings
Diego Mauricio Riaño-Pachón; Luiz Gustavo Guedes Correa; Bernd Mueller-Roeber.
PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss _Physcomitrella patens_ and the rice _Oryza sativa_ spp _indica_. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte...
Tipo: Poster Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1094/version/1
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Are plants with anti-cancer activity resistant to crown gall? : A test of hypothesis Nature Precedings
R Srirama; BT. Ramesha; G. Ravikanth; R. Uma Shaanker; KN Ganeshaiah.
The Crown gall tumour assay (CGTA) is one of several bench top bioassays recommended for the rapid screening of plants with anti-cancer activity. The rationale for the use of the bioassay is that the tumorogenic mechanism initiated in plant tissues by _Agrobacterium tumefaciens_ is in many ways similar to that of animals. Several plant species with anti-cancer activity have already been discovered using this bioassay. However till date no explicit test of an association between anti-cancer activity of plants and their resistance to crown gall formation has been demonstrated. Demonstration of an association could have exploratory potential when searching for plants with anti-cancer activity. In this paper, we determined whether or not a statistically...
Tipo: Manuscript Palavras-chave: Cancer; Pharmacology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1456/version/1
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Age and origin of enigmatic megaherbs from the subantarctic islands Nature Precedings
Steven J. Wagstaff; Ilse Breitwieser; Christopher Quinn; Motomi Ito.
Biogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1272/version/1
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A Meta-analysis of Studies on Plant Growth Rate and Allocation to Roots and Shoots Nature Precedings
Daniel R. Taub.
I performed a meta-analysis of studies examining the relationships among nutrient availability, plant growth rate and allocation to roots vs. shoots. Species characteristic of high fertility habits grew faster than species characteristic of less fertile habitats. While species were highly plastic in root/shoot ratio, there was a strong correlation in root/shoot across fertility levels when plants were grown across fertility gradients. This suggests that the proportional mass allocation to roots is a consistent characteristic of individual species relative to other species. There was no consistent relationship between allocation to roots and either growth rate or the fertility of habitats that species typically are found in.
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/185/version/1
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Current status of herbal and their future perspectives Nature Precedings
Ramar Perumal R. Samy; Ponnampalam Gopalakrishnakone.
Traditional medicine is the synthesis of therapeutic experience of generations of practicing physicians of indigenous systems of medicine. Throughout the history of mankind, many infectious diseases have been treated with herbals. The traditional medicine is increasingly solicited through the tradipractitioners and herbalists in the treatment of infectious diseases. Among the remedies used, plant drugs constitute an important part. A number of scientific investigations have highlighted the importance and the contribution of many plant families i.e. Asteraceae, Liliaceae, Apocynaceae, Solanaceae, Caesalpinaceae, Rutaceae, Piperaceae, Sapotaceae used as medicinal plants. Medicinal plants play a vital role for the development of new drugs (export and import...
Tipo: Manuscript Palavras-chave: Pharmacology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1176/version/1
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Plants at risk from climate change Nature Precedings
Chris Yesson; Alastair Culham.
The popular garden flower Cyclamen grows natively in the Mediterranean. Climate change could make the region unsuitable for 18/21 species in 50 years time. Ant-dispersed Cyclamen can’t hope to migrate to suitable new areas without assistance.

Background: The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group...
Tipo: Poster Palavras-chave: Ecology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/150/version/1
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Biological Activities of Extracts from Sumac (Rhus spp.): A Review Nature Precedings
Sierra Rayne; Giuseppe Mazza.
Sumac is the common name for a genus (Rhus) that contains over 250 individual species of flowering plants in the family Anacardiaceae. These plants are found in temperate and tropical regions worldwide, often grow in areas of marginal agricultural capacity, and have a long history of use by indigenous peoples for medicinal and other uses. The research efforts on sumac extracts to date indicate a promising potential for this plant family to provide renewable bioproducts with the following reported desirable bioactivities: antifibrogenic, antifungal, antiinflammatory, antimalarial, antimicrobial, antimutagenic, antioxidant, antithrombin, antitumorigenic, antiviral, cytotoxic, hypoglycaemic, and leukopenic. As well, the bioactive components can be extracted...
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/631/version/1
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Bio-communication of Plants Nature Precedings
Guenther Witzany.
Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns – mediated by signs.
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Molecular Cell Biology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1429/version/1
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Heterogeneity in Ty1-copia group of retroelements in chickpea (Cicer arietinum) genome Nature Precedings
Manoj K. Rajput; Kailash C. Upadhyaya.
Retrotransposons constitute a major fraction of plant genomes and these elements may have played a significant role in evolution and sequence organization of genomes. In order to access the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequences were amplified from chickpea genome, using the primers derived from two conserved domains of RT region. Thirty-six RT regions from independent amplicons were cloned and sequenced. On the basis of homology of deduced amino acids, the RT sequences could be grouped into three major families. The intra-family divergence at amino acid level ranges from 2 to 19%. Though intra-family RT sequences were conserved but no two sequences were identical. The results indicate a high degree of...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/697/version/1
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Phyloclimatic Modelling: Phylogenies, Palaeo-climate and Environmental Preferences Nature Precedings
Chris Yesson; Alastair Culham.
A new technique is demonstrated for the interpretation of the role played by climate in plant diversity through the optimisation of climate variables on phylogenetic trees. This is achieved by calculating climate preferences for individual species based on established bioclimatic modelling techniques using point
distribution data from distributed sources. We demonstrate a new technique for optimising the component parameters on phylogenetic trees. These parameters can be re-combined into
bioclimatic models for ancestral nodes throughout the phylogenetic tree. The combination of DNA-sequence data and the fossil record is used to establish time-calibrated phylogenies. Using these chronograms, bioclimatic models can in turn...
Tipo: Poster Palavras-chave: Ecology; Plant Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/145/version/1
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A test of _psbK-psbI_ and _atpF-atpH_ as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system Nature Precedings
Renaud R. Y. Lahaye; Vincent Savolainen; Sylvie Duthoit; Olivier Maurin; Michelle van der Bank.
A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene _cox1_, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as _atpF-atpH_ and _psbK-psbI_, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed _matK_ as the best candidate and suggested that in combination with...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1896/version/1
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Integrated disease management using environmental control in tea fields Nature Precedings
Tsuyoshi Tomihama; Nonaka Toshiyuki; Nishi Yatsuka; Arai Kei.
The occurrence of plant disease depends on interactions between the host plant, a pathogen, and the environment in a dynamic called "the disease triangle". Bacterial shoot blight (BSB) disease, caused by _Pseudomonas syringae_ pv. _theae_ (_Pst_), is a major bacterial disease of tea plants in Japan and substantially reduces tea productivity. BSB mainly occurs in the low-temperature season, and lesion formation by _Pst_ is enhanced by both low temperature and the presence of ice nucleation-active _Xanthomonas campestris_ (INAX), which catalyses ice formation at -2 to -4^o^C and is frequently co-isolated with _Pst_ from tea plants^5^. Low temperature is thus the most important environmental factor to influence the incident; however, the...
Tipo: Manuscript Palavras-chave: Microbiology; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1836/version/1
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Selective insectivory in _Nymphaea nouchali_ Burm. f. Nature Precedings
Pundarikakshudu Tetali; Shrikant Sutar; Sujata Tetali.
Carnivorous plants comprise roughly 0.24 percent of the flowering plants, or 640 species represented in 12 families. Yet they are regarded as _miracula naturae_. Over fifty percent of these taxa are represented in a single family, namely Lentibulariaceae. Carnivorous plants are generally insectivorous, and carnivory in flowering plants is generally found in taxa that are adapted to nutrient-deficient habitats. The extra nutrients such plants acquire by special ways serve merely as supplements. The origin and evolution of carnivorous plants is a mystery in the phylogenetic tree of angiosperms, they often appear without a clear linkage. Here, we report that _Nymphaea nouchali_ Burm. f. (a cultivar of var. cernua), a large aquatic member of the family...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1817/version/1
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Historical deforestation patterns and the conservation value of church forests in the northern Ethiopian highlands Nature Precedings
Raf Aerts; Richard Pankhurst; Koen Van Overtveld; Eva J. J. November; Martin Hermy; Bart Muys.
Mountain forest plants have a limited capacity for migration because altitudinal gradients usually set strict limits to plant species’ ranges and often present physical barriers against dispersal. Innate ‘islands’ of biodiversity, mountain forests are therefore particularly vulnerable to the effects of climatic change and habitat fragmentation, both key drivers of global species loss. Conservation of these ecosystems must for that reason rely on protecting not only large fragments but also small habitat patches and relictual vegetation along a wide altitudinal range.
When large fragments in such ecosystems are no longer available, small fragments become an environmental priority. Striking examples of...
Tipo: Presentation Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1786/version/1
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