PAPADAKIS NEAREST NEIGHBOR ANALYSIS OF YIELD IN AGRICULTURAL EXPERIMENTS

Papadakis analysis, originally proposed by Papadakis in 1937 belongs to a larger class of methodologies called the nearest neighbor analysis which is primarily based on the fact that plots in close proximity ( neighbors ) are exposed to similar environmental conditions and therefore, for a given plot, information from its neighboring plots could be used for adjustment of its response for spatial variability. The basic theory behind the application of Papadakis methodology to field trials is relatively simple. It is based on an analysis of covariance where the covariate is an index of fertility environment), and the response is some observable trait (e.g., grain yield), which is adjusted up or down to reflect the effect due to spatial variability. There have been several references in the literature to application of Papadakis methodology to field trials where the analysis is routinely carried out on data coming from a replicated design within a testing location. The application that is presented here is an exception to the rule in that the analysis is conducted on multi-location data with single replication per location. In plant breeding industry, a recent trend has been to move towards one-replicate testing system to maximize the coverage of the testing environments. Note that for a one-replicate test, no design such as a Lattice, can be used for adjustment of the observations for spatial variability. We start with describing the theory and methodology behind the proposed Papadakis analysis for multilocation data. Several practical problems such as impact of missing values on Papadakis covariate, choice of homogeneous vs. heterogeneous slope coefficient, and effect of influential observations, etc. are discussed and solutions are proposed. Finally, results from several validation studies on com yield data, including comparison to lattice adjusted plot values and ANOV A on adjusted vs. unadjusted data are presented to demonstrate the benefit from the proposed procedure

Micropropagation and conservation of selected endangered anticancer medicinal plants from the Western Ghats of India

Globally, cancer is a constant battle which severely affects the human population. The major limitations of the anticancer drugs are the deleterious side effects on the quality of life. Plants play a vital role in curing many diseases with minimal or no side effects. Phytocompounds derived from various medicinal plants serve as the best source of drugs to treat cancer. The global demand for phytomedicines is mostly reached by the medicinal herbs from the tropical nations of the world even though many plant species are threatened with extinction. India is one of the mega diverse countries of the world due to its ecological habitats, latitudinal variation, and diverse climatic range. Western Ghats of India is one of the most important depositories of endemic herbs. It is found along the stretch of south western part of India and constitutes rain forest with more than 4000 diverse medicinal plant species. In recent times, many of these therapeutically valued herbs have become endangered and are being included under the red-listed plant category in this region. Due to a sharp rise in the demand for plant-based products, this rich collection is diminishing at an alarming rate that eventually triggered dangerous to biodiversity. Thus, conservation of the endangered medicinal plants has become a matter of importance. The conservation by using only in situ approaches may not be sufficient enough to safeguard such a huge bio-resource of endangered medicinal plants. Hence, the use of biotechnological methods would be vital to complement the ex vitro protection programs and help to reestablish endangered plant species. In this backdrop, the key tools of biotechnology that could assist plant conservation were developed in terms of in vitro regeneration, seed banking, DNA storage, pollen storage, germplasm storage, gene bank (field gene banking), tissue bank, and cryopreservation. In this chapter, an attempt has been made to critically review major endangered medicinal plants that possess anticancer compounds and their conservation aspects by integrating various biotechnological tool

Expression of a Truncated ATHB17 Protein in Maize Increases Ear Weight at Silking

<div><p><i>ATHB17</i> (AT2G01430) is an Arabidopsis gene encoding a member of the α-subclass of the homeodomain leucine zipper class II (HD-Zip II) family of transcription factors. The ATHB17 monomer contains four domains common to all class II HD-Zip proteins: a putative repression domain adjacent to a homeodomain, leucine zipper, and carboxy terminal domain. However, it also possesses a unique N-terminus not present in other members of the family. In this study we demonstrate that the unique 73 amino acid N-terminus is involved in regulation of cellular localization of ATHB17. The ATHB17 protein is shown to function as a transcriptional repressor and an EAR-like motif is identified within the putative repression domain of ATHB17. Transformation of maize with an ATHB17 expression construct leads to the expression of ATHB17Δ113, a truncated protein lacking the first 113 amino acids which encodes a significant portion of the repression domain. Because ATHB17Δ113 lacks the repression domain, the protein cannot directly affect the transcription of its target genes. ATHB17Δ113 can homodimerize, form heterodimers with maize endogenous HD-Zip II proteins, and bind to target DNA sequences; thus, ATHB17Δ113 may interfere with HD-Zip II mediated transcriptional activity via a dominant negative mechanism. We provide evidence that maize HD-Zip II proteins function as transcriptional repressors and that ATHB17Δ113 relieves this HD-Zip II mediated transcriptional repression activity. Expression of ATHB17Δ113 in maize leads to increased ear size at silking and, therefore, may enhance sink potential. We hypothesize that this phenotype could be a result of modulation of endogenous HD-Zip II pathways in maize.</p></div

List of differentially expressed genes in ear inflorescence in common between two <i>ATHB17</i> events.

<p>Table lists the fold change (Fc), raw and fdr p-values for common genes in each event.</p

List of differentially expressed genes in ear in common between two <i>ATHB17</i> events.

<p>Table lists the fold change (Fc), raw and fdr p-values for common genes in each event.</p

Phenology of <i>ATHB17</i> events and control.

<p>Two independent <i>ATHB17</i> events in three hybrids were used in physiological studies conducted in 2011 and 2012 under standard agricultural practices (SAP) for corn production in the Central Corn Belt. The number of days to 50% silking and anthesis were measured and the number of days between anthesis and silking was calculated (ASI) each year for physiological studies conducted under standard agronomic practices conditions. Differences in phenology between <i>ATHB17</i> events and control were determined using an across year combined analysis using a mixed model ANOVA. N denotes the number of data points included per entry in the statistical analysis. Number of event data points were within ±3 of control data points. Results for individual hybrids per year are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094238#pone.0094238.s004" target="_blank">Table S2</a>.</p

ATHB17 is a member of the α subclass within the HD-Zip II protein family.

<p>(A) represents the dendrogram and the domain architecture of the ATHB17 homologs. ATHB17 contains a typical homeodomain (HD; blue shading) and a leucine zipper motif (LZ; green shading) adjacent to the C-terminus of the HD. Red bars indicate conserved cysteines in the C-terminus. (B) shows the protein sequence of ATHB17. ATHB17 contains a unique N-terminal extension (red shading) rich in cysteines and tyrosines. Additional structural feature identified for ATHB17 is a nuclear localization signal (red boxes). Downstream of the LZ motif is a putative redox sensing motif (CPXCE; red letters).</p

Full- length ATHB17 protein functions as transcriptional repressor and ATHB17Δ113 can relieve repression caused by full-length ATHB17 protein.

<p>Maize mesophyll protoplasts were transformed (A) with 4 µg cells of reporter (Class II::GUS, Class I::GUS or No BS::GUS) and 0–5 µg cells of effector (Full-length ATHB17) or 5 µg of ATHB17Δ113 and <i>Renilla</i> luciferase (B) with 4 µg reporter (Class II::GUS, Class I::GUS or No BS::GUS), 0–5 µg ATHB17Δ113, and 0 (grey bars) or 0.2 µg (blue bars) of ATHB17 full length. DNA amounts are per 320,000 cells. After 18 h, cells were assayed for GUS and luciferase expression. GUS values were divided by luciferase internal control values for each well and normalized to respective GFP samples. Bars are means and error bars represent 1 SD.</p

ATHB17Δ113 can bind both Class II and Class I DNA targets and ATHB17Δ113 containing V182A-Q185A-N186A mutation cannot bind Class II DNA target in <i>in vitro</i> assay (measured by Surface Plasmon Resonance (SPR).

<p>Binding affinities and Kinetic constants of ATHB17Δ113 interacting with Class I and Class II type DNA, measured by Biacore 2000, globally fitted. SPR measurements with Biacore 2000 were at 25°C in HBS-EP, 100 ug/ml BSA (10 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.005% Tween-20,100 ug/ml BSA). Equilibrium dissociation constant K_D = k_off/k_on.</p

ATHB17Δ113 is localized to nucleus.

<p>Fluorescence micrographs of maize leaf protoplasts transformed with (A) GFP alone, (B) AtCBF3 fused to GFP as positive control for nuclear localization or (C) ATHB17Δ113 fused with GFP. Protoplasts from each construct were analyzed by laser scanning microscopy for GFP and chlorophyll fluorescence and acquired images were merged on bright-field image using the Image examiner (See Materials and Methods for details).</p