Generating normal networks via leaf insertion and nearest neighbor interchange

Background Galled trees are studied as a recombination model in theoretical population genetics. This class of phylogenetic networks has been generalized to tree-child networks and other network classes by relaxing a structural condition imposed on galled trees. Although these networks are simple, their topological structures have yet to be fully understood. Results It is well-known that all phylogenetic trees on n taxa can be generated by the insertion of the n-th taxa to each edge of all the phylogenetic trees on n−1 taxa. We prove that all tree-child (resp. normal) networks with k reticulate nodes on n taxa can be uniquely generated via three operations from all the tree-child (resp. normal) networks with k−1 or k reticulate nodes on n−1 taxa. Applying this result to counting rooted phylogenetic networks, we show that there are exactly $\frac {(2n)!}{2^{n} (n-1)!}-2^{n-1} n!$(2n)!2n(n−1)!−2n−1n! binary phylogenetic networks with one reticulate node on n taxa. Conclusions The work makes two contributions to understand normal networks. One is a generalization of an enumeration procedure for phylogenetic trees into one for normal networks. Another is simple formulas for counting normal networks and phylogenetic networks that have only one reticulate node.

Metode inokulasi buatan untuk menguji infeksi Peronosclerospora maydis penyebab penyakit bulai tanaman jagung

Keberadaan penyakit bulai akibat Peronosclerospora maydis pada tanaman jagung mampu menyebabkan kehilangan hasil hingga 100%. Pengendalian penyakit bulai dengan menggunakan varietas tahan dinilai cukup efektif. Di dalam pengembangan varietas tahan, seleksi ketahanan calon varietas baru harus dilakukan dan hal ini akan melibatkan inokulasi buatan. Tujuan dari penelitian ini adalah untuk mendapatkan metode inokulasi buatan Peronosclerospora maydis yang efektif pada tanaman jagung pada skala rumah kaca. Penelitian dilaksanakan di Laboratorium Bioteknologi Proteksi Tanaman dan rumah kaca Departemen Hama dan Penyakit Tumbuhan, Fakultas Pertanian, Universitas Padjadjaran pada bulan Oktober hingga Desember 2018. Bahan tanaman yang diinokulasikan berupa kecambah dan bibit tanaman jagung. Metode inokulasi buatan yang diujikan terdiri atas: (1) Sisip daun terinfeksi bulai pada kecambah (SD), (2) Semprot suspensi konidia pada kecambah (SI), (3) Sisip daun bergejala bulai + semprot suspensi konidia pada kecambah (SS), (4) Rendam kecambah pada suspensi konidia (RS), (5) Semprot suspensi konidia pada bibit (SB), dan dua perlakuan tanpa inokulasi (kontrol). Dari hasil percobaan metode sisip daun (SD) menyebabkan 83,3% tanaman jagung terinfeksi bulai dan dinilai sebagai metode inokulasi buatan yang efisien.Kata kunci: bulai, jagung, inokulasi buatan, Peronosclerospora maydis. ABSTRACTDowny mildew disease caused by Peronosclerospora maydis in maize plants can cause yield loss up to 100%. Disease management of downy mildew by using resistant varieties is considered quite effective. One of the steps to develop resistant varieties is resistance testing of the new variety candidates that involve artificial inoculation. The purpose of this study was to obtain an effective artificial inoculation method of Peronosclerospora maydis in maize plants in greenhouse. The research was conducted at the Laboratory of Biotechnology of Plant Protection and Glasshouse Department of Plant Pests and Diseases, Agriculture Faculty, Universitas Padjadjaran from October to December 2018. The plant materials used for inoculation were sprout and seedling of maize plant. The artificial inoculation methods tested were (1) infected leaf insertion among the sprouts (SD), (2) conidia suspension spraying on the sprouts (SI), (3) infected leaf insertion + conidia suspension spraying on the sprouts (SS), (4) sprout soaking in conidia suspension (RS), (5) conidia suspension spraying on the seedling (SB), and two treatments without inoculation (controls). The result showed that the insertion of infected leaves among the sprouts (SD) treatment resulted in 83.3% of infected maize plants by the downy mildew and was considered as the most efficient inoculation method.

Non-intersecting leaf insertion algorithm for tree structure models

We present an algorithm and an implementation to insert broadleaves or needleleaves into a quantitative structure model according to an arbitrary distribution, and a data structure to store the required information efficiently. A structure model contains the geometry and branching structure of a tree. The purpose of this work is to offer a tool for making more realistic simulations of tree models with leaves, particularly for tree models developed from terrestrial laser scanning (TLS) measurements. We demonstrate leaf insertion using cylinder-based structure models, but the associated software implementation is written in a way that enables the easy use of other types of structure models. Distributions controlling leaf location, size and angles as well as the shape of individual leaves are user definable, allowing any type of distribution. The leaf generation process consist of two stages, the first of which generates individual leaf geometry following the input distributions, while in the other stage intersections are prevented by carrying out transformations when required. Initial testing was carried out on English oak trees to demonstrate the approach and to assess the required computational resources. Depending on the size and complexity of the tree, leaf generation takes between 6 and 18 min. Various leaf area density distributions were defined, and the resulting leaf covers were compared with manual leaf harvesting measurements. The results are not conclusive, but they show great potential for the method. In the future, if our method is demonstrated to work well for TLS data from multiple tree types, the approach is likely to be very useful for three-dimensional structure and radiative transfer simulation applications, including remote sensing, ecology and forestry, among others.

Phyllotactic transitions in seedlings: the case of Thuja occidentalis

The main goal of this study was to examine different phyllotactic patterns and pattern transitions in seedlings of eastern white cedar ( Thuja occidentalis L.). Four phyllotactic patterns were observed on the main stem of T. occidentalis: tetracussate, tricussate, (3, 5) spiral, and decussate. Only one phyllotactic pattern was observed on the side branches of T. occidentalis: decussate. Four types of phyllotactic pattern transition were observed: tetracussate to decussate, tetracussate to tricussate, tricussate to (3, 5) spiral, and (3, 5) spiral to decussate. For each phyllotactic pattern, the following phyllotactic parameters were examined using histological sections: divergence angle, plastochrone ratio, leaf insertion angle, parameter Г, and apical angle of the shoot apical meristem (SAM). Even though they varied widely, the phyllotactic parameters measured in T. occidentalis seem to fall within ranges observed in other plants for specific phyllotactic patterns. The results indicate that it is not possible to discriminate between the four different phyllotactic patterns observed on T. occidentalis by using the plastochrone ratio, leaf insertion angle, parameter Г, or apical angle of the SAM. In contrast to continuous transitions, where there is a good correlation between phyllotactic parameters, there was no correlation between the phyllotactic pattern (characterized by a given divergence angle) and other phyllotactic parameters in the discontinuous transitions observed in T. occidentalis.

Rice grown in nutrient solution with doses of manganese and silicon

Although silicon is not recognized as a nutrient, it may benefit rice plants and may alleviate the Mn toxicity in some plant species. The dry matter yield (root, leaf, sheaths and leaf blade) and plant architecture (angle of leaf insertion and leaf arc) were evaluated in rice plants grown in nutrient solutions with three Mn doses, with and without Si addition. The treatments were arranged in a 2 x 3 factorial [with and without (2 mmol L-1) Si; three Mn doses (0.5; 2.5 and 10 µmol L-1)], in a randomized block design with 4 replications. The experimental unit was a 4 L plastic vase with 4 rice (Metica-1 cultivar) plants. Thirty nine days after keeping the seedlings in the nutrient solution the plant dry matter yield was determined; the angle of leaf insertion in the sheath and the leaf arc were measured; and the Si and Mn concentrations in roots, sheaths and leaves were determined. The analysis of variance (F test at 5 and 1 % levels) and the regression analysis (for testing plant response to Mn with the Si treatments) were performed. The Si added to the nutrient solution increased the dry matter yield of roots, sheaths and leaf blades and also decreased the angle of leaf blade insertion into the sheath and the foliar arc in the rice plant. Additionally, it ameliorated the rice plant architecture which allowed an increase in the dry matter yield. Similarly, the addition of Mn to the solution improved the architecture of the rice plants with gain in dry matter yield. As Si was added to the nutrient solution, the concentration of Mn in leaves decreased and in roots increased thus alleviating the toxic effects of Mn on the plants.

Comparing Leaf and Root Insertion

We consider two ways of inserting a key into a binary search tree: leaf insertion which is the standard method, and root insertion which involves additional rotations. Although the respective cost of constructing leaf and root insertion binary search trees trees, in terms of comparisons, are the same in the average case, we show that in the worst case the construction of a root insertion binary search tree needs approximately 50% of the number of comparisons required by leaf insertion.

In vitro digestibility response of cocksfoot (Dactylis glomerata L.) to growth and defoliation: a simple model

Herbage digestibility, which to a large extent governs the animal's intake, is not easily predicted for grazing animals, and can vary due to different grazing managements. The objective of this study was to build a model for a range of defoliation managements, which takes account of vegetative grass tiller structure, rather than dates of cutting or grazing, as done usually. An experiment was conducted in 1997, near Toulouse, to examine the digestibility of cocksfoot whole lamina and lamina segments (15 cm) for three defoliation regimes. These regimes mimicked severe and lenient intermittent defoliations plus a frequent defoliation treatment over a six-week period. Data were collected for (i) lamina mass and digestibility for the youngest expanded lamina, (ii) lamina appearance rate, lamina and sheath lengths.Laminae digestibility, measured over time, varied greatly with the defoliation regime both for the youngest full expanded lamina and all laminae on a tiller. Digestibility of the youngest fully expanded lamina decreased from one leaf insertion level to the next, but this decrease was lowest when the defoliation regime was frequent. There was also a consistent decrease in the digestibility of a lamina from its tip to its base. Sheath and lamina lengths varied with treatment in a different way to lamina digestibility. During frequent defoliation, sheath and lamina lengths both increased slightly while they showed substantial increases in the two other treatments. Lamina length increased from one insertion level to the next, and resulted in the addition of less digestible lamina segments rather than reducing overall lamina digestibility. Sheath length, through its influence on leaf appearance rate and lamina length, could be used to predict the digestibility of laminae over time according to leaf insertion level and the difference in the digestibility observed from the tip to the base of a particular lamina. Sheath length could therefore provide a basis for predicting the time course of grass digestibility for different combinations of defoliation frequency and height.