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12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era Nature Precedings
Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech; Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. 
We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5466/version/1
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A bestiary of non-linear functions for growth analysis Nature Precedings
C. E. Timothy Paine; Toby Marthews; Deborah Vogt; Drew Purves; Mark Rees; Andy Hector; Lindsay Turnbull.
Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.
A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear,...
Tipo: Presentation Palavras-chave: Ecology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5257/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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A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From Seeds Nature Precedings
Israr Khan; Muhammad Shuaib; Sikandar Khan; Muhammad Amir Zia; Haji Akbar.
Canola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation. Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4781/version/2
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A New Behavior of Nuclei during Mitosis of Lilium Hybrids Nature Precedings
Zheng Sixiang; Liu Feihu; Zhang Chaojun; Chen Zhilin; Ma Yuhua; Meng Pinghong; Zhao Yan.
Mitosis is nuclear division plus cytokinesis,and produces two identical daughter cells during prophase, prometaphase, metaphase, anaphase, and telophase. However, a new nucleus behavior in interspecific hybrid progenies of Lilium was observed in our experiment. Very unusual behaviors of nuclei surprisingly presented during the mitosis, such as sprouting or germination, tube-like elongation, penetrating cell membrane into a neighbor cell, the top of nuclei tube expanding, intruding and splitting of the tube-like nucleus, and micronucleus formation, and so on. Furthermore, the tetrad of meiosis was founded in mitosis of root.

Routine of the unusual nucleus behaviors observed in our experiment may be summarized as nucleus...
Tipo: Manuscript Palavras-chave: Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4631/version/1
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A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements- (v.4) Nature Precedings
Valentin Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional “wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6231/version/4
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A novel superior factor widely controlling the rice grain quality Nature Precedings
Kao-Chih She; Hiroaki Kusano; Kazuyoshi Koizumi; Hiromoto Yamakawa; Makoto Hakata; Tomohiro Imamura; Masato Fukuda; Natsuka Naito; Yumi Tsurumaki; Ken'ichiro Matsumoto; Mari Kudoh; Eiko Itoh; Shoshi Kikuchi; Naoki Kishimoto; Junshi Yazaki; Tsuyu Ando; Masahiro Yano; Takashi Aoyama; Tadamasa Sasaki; Hikaru Satoh; Hiroaki Shimada.
Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to symptoms...
Tipo: Manuscript Palavras-chave: Plant Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3283/version/1
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A similarity criterion for forest growth curves Nature Precedings
Georgii A. Alexandrov; Georgy S. Golitsyn.
Comparison of forest growth curves has led many to the conclusion that there is a similarity between forest stands growing in different conditions. Here we treat the same subject from the viewpoint of similarity theory. Our goal is to form a dimensionless ratio of biophysical entities that could parameterize the diversity of forest growth curves. (Such ratios are called similarity criteria.) Pursuing this goal, we focus on the analogy between tree crown growth and atomic explosion. A blast wave is formed when the rate of energy release is much higher than the rate of energy dissipation. The difference between the rates of energy release and dissipation is the essence of this phenomenon. The essential feature of crown growth is the difference between the...
Tipo: Manuscript Palavras-chave: Ecology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6561/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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A Tobacco Homolog of DCN1 is Involved in Cellular Reprogramming and in Developmental Transitions Nature Precedings
Julia Hosp; Alexandra Ribarits; Katarzyna Szaszka; Yongfeng Jin; Alisher Tashpulatov; Marina Baumann; Tatiana Resch; Christina Friedmann; Elisabeth Ankele; Viktor Voronin; Klaus Palme; Alisher Touraev; Erwin Heberle-Bors.
Plant proteomes show remarkable plasticity in reaction to environmental challenges and during developmental transitions. Some of this adaptability comes from ubiquitin-mediated protein destruction regulated by cullin-RING E3 ubiquitin ligases (CRLs). CRLs are activated through modification of the cullin subunit with the ubiquitin-like protein RUB/NEDD8 by an E3 ligase called defective in cullin neddylation 1 (DCN1). Here we show that tobacco DCN1 binds ubiquitin and RUB/NEDD8, and associates with cullin. When knocked down by RNAi, tobacco pollen formation stopped and zygotic embryogenesis was blocked around the globular stage. Additionally, we found that RNAi of DCN1 inhibited the stress-triggered reprogramming of cultured microspores from their intrinsic...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5728/version/1
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A unified mechanistic model of niche, neutrality and violation of the competitive exclusion principle Nature Precedings
Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10% difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%)....
Tipo: Manuscript Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7089/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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Allergological and toxicological risk assessment of genetically modified (GM) plants - Development of a model system Nature Precedings
Alain Steinmann; Kristin Entzian; Birgit Grümmer; Udo Meyer.
Technical advances in biotechnology lead to a rising number of genetically modified plants and derived food and feed. Therefore, the international interest in adequate and standardized analytical methods increases to assess health risks in a rapid and low cost manner.
To address this issue a decision support system (DSS), which will be based on baseline data and thresholds of key parameters, is going to be established in the framework of a joint project (BioOK). Determination of the potential allergenicity or toxicity of novel proteins caused by the genetic modification compared to near isogenic variants (NIV) is a key issue in this context. For the development of DSS the model plant “potato” was used to compare...
Tipo: Poster Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4441/version/1
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Altered copy gene function in plants following total intron replacement in precursor RNA Nature Precedings
Drew Schwartz.
Evidence is presented for two novel genetic mechanisms: total intron replacement in transcribedprecursor RNA by multiple short sequences and reverse transcription of the precursor RNA followedby incorporation into the genome as copy genes, some of which have acquired an altered function.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Plant Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4307/version/1
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Ambiguous Dependence Of Minimal Plant Generation Time On Nuclear DNA Content Nature Precedings
Victor B. Ivanov.
AMBIGUOUS DEPENDENCE OF MINIMAL PLANT GENERATION TIME ON NUCLEAR DNA CONTENT Victor B. Ivanov The minimum generation time (MGT) of plant development was suggested to depend on nuclear DNA content, which varies in plants over wide limits1. In ephemeral species with the shortest MGT, the average C values were significantly lower than in annual species, whereas the average C values in annual species were lower than those in perennial plants. However, nobody has paid attention to the ratio of annual to perennial species number as a function of C values. Here I show that with increasing C the ratio of annual to perennial species increases to C values equal to 7-8 pg (monocots) and 6-7 pg (eudicots) and then decreases and that the fraction of annuals is abundant...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4943/version/1
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'Kuthiru' and 'Orkayama' – Newly Identified Genetic Resources from Kerala, India for Salinity Tolerance in Indica Rice Nature Precedings
Vanaja Taliyil; K P. Mammootty.
Existence of genetic variability for salt tolerance within species is of paramount importance in crop improvement program. Pokkali land race of Kerala, India is the international donor parent of most of the salinity tolerance breeding programs in rice. Here we report two new genetic resources, ‘Kuthiru’ and ‘Orkayama’ for salinity tolerance, from Kaipad saline tracts of Kerala. They differ in their morphological, physico-chemical characteristics and cooking qualities. Panicles of these cultivars are long with bold grains. Duration of ‘Kuthiru’ is 110 -120 days, and that of ‘Orkayama’ is 135 -140 days. Molecular analysis revealed that the salinity tolerance mechanism...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4561/version/1
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An innovative method for the biological control of Alternanthera philoxeroides Nature Precedings
Yusong Cao; Huiming Wang.
Biological invasion has become a serious global environmental problems and been considered as an important component of global change^1-2^. Invasions by alien species can have an impact at several levels of ecological complexity from genes to ecosystems^3-4^. Invasive alien species had seriously threated the biodiversity and natural ecosystems in China^5^, and caused economic losses by more than US$7 billion every year^6^. Alternanthera philoxeroides, commonly known as Alligator weed, is an invasive amphibious plant^7^. The effect of physical methods such as mechanical or artificial salvage, removal of A. philoxeroides were very limited. Moreover, these measure should be carried out very carefully or would easy lead to its rebound^8^. The mainly biological...
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5267/version/1
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Analysis of plant metabolites – the baseline-threshold principle Nature Precedings
Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.

The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4439/version/1
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Analysis of plant metabolites – the baseline-threshold principle Nature Precedings
Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.

The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4439/version/2
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Antidiabetic, Anti-hyperlipidemic & Hepatoprotective effect of a Polyherbal Unani formulation “Qurs Tabasheer” in STZ-diabetic wistar rats Nature Precedings
Danish Ahmed; Manju Sharma; Alok Mukerjee; Raja Kamal Kant; Vikas Kumar.
The present study was undertaken to evaluate the antihyperglycemic, antihyperlipidemic and hepatoprotective effect of a traditional unani formulation “Qurs Tabasheer” in streptozotocin (STZ) induced diabetic wistar rats. Up until now, no study was undertaken to appraise the efficacy of “Qurs Tabasheer” in the diabetic rats. Qurs Tabasheer is a unani formulation restraining preparations from six various herbs namely Tukhme Khurfa (Portulaca oleracea seed), Gule Surkh (Rosa damascena flower), Gile armani (Arminium bole), Gulnar (Punica granatum flower), Tabasheer (Bambusa arundinasia dried exudate on node), Tukhme Kahu (Lactuca sativa Linn seed). The effect of Qurs Tabasheer was assessed in STZ (60 mg/kg, i.p...
Tipo: Manuscript Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7056/version/1
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