Seema Jaggi

Biocontrol potential of cyanobacterial metabolites against damping off disease caused by Pythium aphanidermatum in solanaceous vegetables

An investigation was undertaken to explore the biocidal efficacy of fungicidal compound(s) produced by Calothrix elenkenii against damping-off disease in three vegetable crops-tomato, chilli and brinjal. Treatments included application of seeds soaked in water (control), culture filtrate and ethyl acetate extract of Calothrix elenkenii and Metalaxyl in potting mix inoculated with Pythium aphanidermatum in plastic pots. The observations taken after a period of four weeks revealed the superiority of seed treatment with ethyl acetate extracts, in terms of percent mortality and plant parameters. ANOVA revealed that the treatments, crops (tomato, chilli and brinjal) and their interactions exerted a significant influence on the parameters analyzed. Chilli recorded the highest percentage of survivors and responded best to the seed treatment with ethyl acetate extract of Calothrix elenkenii. Future work is being undertaken towards formulation of a biocontrol agent using Calothrix elenkenii and understanding the molecular basis for the biocontrol properties.

On totally balanced block designs for competition effects

Competition between neighbouring units in field experiments is a serious source of bias. The study of a competing situation needs construction of an environment in which it can happen and the competing units have to appear in a predetermined pattern. This paper describes methods of constructing incomplete block designs balanced for neighbouring competition effects. The designs obtained are totally balanced in the sense that all the effects, direct and neighbours, are estimated with the same variance. The efficiency of these designs has been computed as compared to a complete block design balanced for neighbours and a catalogue has also been prepared.

Minimal balanced repeated measurements designs

Experimental designs in which treatments are applied to the experimental units, one at a time, in sequences over a number of periods, have been used in several scientific investigations and are known as repeated measurements designs. Besides direct effects, these designs allow estimation of residual effects of treatments along with adjustment for them. Assuming the existence of first-order residual effects of treatments, Hedayat & Afsarinejad (1975) gave a method of constructing minimal balanced repeated measurements [RM(v,n,p)] design for v treatments using n=2v experimental units for p [=(v+1)/2] periods when v is a prime or prime power. Here, a general method of construction of these designs for all odd v has been given along with an outline for their analysis. In terms of variances of estimated elementary contrasts between treatment effects (direct and residual), these designs are seen to be partially variance balanced based on the circular association scheme.

Optimal Circular Block Designs for Neighbouring Competition Effects

Abstract Competition or interference occurs when the responses to treatments in experimental units are affected by the treatments in neighbouring units. This may contribute to variability in experimental results and lead to substantial losses in efficiency. The study of a competing situation needs designs in which the competing units appear in a predetermined pattern. This paper deals with optimality aspects of circular block designs for studying the competition among treatments applied to neighbouring experimental units. The model considered is a four-way classified model consisting of direct effect of the treatment applied to a particular plot, the effect of those treatments applied to the immediate left and right neighbouring units and the block effect. Conditions have been obtained for the block design to be universally optimal for estimating direct and neighbour effects. Some classes of balanced and strongly balanced complete block designs have been identified to be universally optimal for the estimation of direct, left and right neighbour effects and a list of universally optimal designs for v<20 and r<100 has been prepared.

Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach

Abstract Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product, which may be proteins. A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is statistically significant. To identify differentially expressed genes between two conditions, it is important to find statistical distributional property of the data to approximate the nature of differential genes. In the present study, the focus is mainly to investigate the differential gene expression analysis for sequence data based on compound distribution model. This approach was applied in RNA-seq count data of Arabidopsis thaliana and it has been found that compound Poisson distribution is more appropriate to capture the variability as compared with Poisson distribution. Thus, fitting of appropriate distribution to gene expression data provides statistically sound cutoff values for identifying differentially expressed genes.

Neighbor-Balanced Row-column Designs

In this article, row-column designs incorporating directional neighbor effects have been studied. A row-column design is said to be neighbor balanced if every treatment has all other treatments appearing as a neighbor a constant number of times. We considered here three different situations under row-column setup incorporating neighbor effects viz., row-column design with one-sided neighbor effect, two-sided neighbor effect, and four-sided neighbor effect. The information matrices for all the situations for estimating the direct and neighbor effects of treatments have been derived. Methods of constructing neighbor-balanced row-column designs have been developed and its characterization properties have been studied.

Web generation of experimental designs balanced for indirect effects of treatments (WEB-DBIE)

Online software to generate designs balanced for indirect effects of treatments.It consists of randomized layout of Neighbour Balanced and Crossover Designs.Online catalogue of designs within a permissible range of parameters is provided.This software (WEB-DBIE) is deployed at www.iasri.res.in/webdbie.It is freely available for the researchers and students working in this area. Indirect effects are effects that occur in an experiment due to the units which are adjacent (spatially or temporally) to the unit being observed. Spatial indirect effects arise due to the treatments applied to the adjacent neighbouring units/plots and the designs so developed are called Neighbour Balanced Designs (NBDs). Whereas temporal indirect effects occur because of the carryover or residual effects in the periods following the periods of their direct application and the designs considering temporal effects are called Crossover Designs. A large number of such designs have been developed in the literature. For ready referencing and potential use of these designs, online software for generation of randomized layout of these designs is highly desirable. This paper describes the development of a web solution for generation of NBDs and Crossover Designs using client-server architecture along with an online catalogue of the designs within a permissible range. Designs generated through this software have wide applications in agricultural experiments, forestry and agro-forestry trials, polycross nurseries, serological experiments, animal nutritional trials, sensory evaluations, clinical trials, etc. WEB-DBIE is accessible any time from arbitrary platforms through internet. This software provides freely available solution for the researchers and students working in this area.

Universally optimal second order neighbour designs

This paper deals with optimality aspects of complete block designs with interference effects arising from the neighbouring units up to distance 2 (first and second order) from one side. Conditions have been obtained for the block design to be universally optimal for estimating direct and interference effects. Some classes of balanced and strongly balanced complete block designs have been identified to be universally optimal for the estimation of direct effects, first order neighbour effects and second order neighbour effects.

Tetrahedral and cubical association schemes with related PBIB(3) designs

Here, two three-class association schemes called tetrahedral association scheme and cubical association scheme have been proposed along with methods of constructing partially balanced incomplete block designs based on these schemes. Designs based on cubical association scheme are found to be resolvable. An outline of the method of analysis of the designs has also been presented together with a list of PBIB(3) designs obtained using the proposed methods for number of treatments v < 100. The proposed designs are seen to be more efficient than the circular lattices (PBIB(3) designs) with the same number of experimental units for the estimation of elementary treatment effect contrasts.

On the generation of cost effective response surface designs

SAS Macros for the generation of Cost Effective Response Surface Designs.Generation of Plackett-Burman Designs, CCD and BBD with minimum level changes.Output can be saved in MS-Word Format.Macro developed is freely available for the researchers working in this area. Run order consideration for mixed factorial, fractional factorial and confounded factorial have been studied by several authors in depth, but is lacking for Response Surface Designs (RSDs) except the results obtained by Quinlan and Lin (2015) for Plackett-Burman Design, a commonly used first order response surface design for screening purpose. Second Order Response Surface Designs (SORDs) are used to explore relationship between the response variable and the input variables and to find out the optimum input combinations to achieve a desired response. In this paper, we aim to find out optimal run orders with respect to minimizing level changes using a computer programme. Minimizing the level changes implies the minimization of experimental cost. Generation of four classes of designs viz., Plackett-Burman Design, Cost-effective Central Composite Design (CCD) with full factorial as well as fractional factorial points and Cost-effective Box Behnken Design (BBD) have been described through Macros developed using SAS IML.