Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes

Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species

A STUDY ON NON SPLIT DOMINATION NUMBER

The word “mathematics” comes from the Greek word “Mathema” which means science, knowledge or learning; Mthematiko’s means fond of learning. Today, the term refers to specific body of knowledge - the deductive study of quantity, structure, space and change. Mathematics links the abstract world of mental concepts to real world of physical things. Graph theory is one of the most developing branches of mathematics with many modern applications. Its basic ideas were introduced in the 18th century, by the great Swiss mathematician Leonard Euler. Certain problems in physics, chemistry, communications science, computer technology, genetics, psychology, sociology and linguistics can be formulated as problems in graph theory. Also it plays an important role in several areas of computer science such as switching theory and logic design, Artificial Intelligence, formal languages, operating system and information such as group theory, metric theory, probability and topology have interactions with graph theory. The concept of non split domination in graphs helps to find a subset, which covers the whole graph in unit distance. A communication network can be represented by a connected graph G, where the vertices of G represent processors and edges represent bi-directional communication channels. A dominating set in a graph can be interpreted as a set of processors from which information can be passed on to all the other processors. Hence determination of non split domination parameter of a graph is an important problem. The global non split domination number, cycle non split domination number and the path non split domination number was introduced by kulli and Nandargi. The block non split domination number was introduced by kulli and Janakiram. The total dominating set concept was introduced by Janakiram, soner and chaluvar

Patterns of divergence of a large family of nodule cysteine‐rich peptides in accessions of<i><scp>M</scp>edicago truncatula</i>

The nodule cysteine-rich (NCR) groups of defensin-like (DEFL) genes are one of the largest gene families expressed in the nodules of some legume plants. They have only been observed in the inverted repeat loss clade (IRLC) of legumes, which includes the model legume Medicago truncatula. NCRs are reported to play an important role in plant–microbe interactions. To understand their diversity we analyzed their expression and sequence polymorphisms among four accessions of M. truncatula. A significant expression and nucleotide variation was observed among the genes. We then used 26 accessions to estimate the selection pressures shaping evolution among the accessions by calculating the nucleotide diversity at non-synonymous and synonymous sites in the coding region. The mature peptides of the orthologous NCRs had signatures of both purifying and diversifying selection pressures, unlike the seed DEFLs, which predominantly exhibited purifying selection. The expression, sequence variation and apparent diversifying selection in NCRs within the Medicago species indicates rapid and recent evolution, and suggests that this family of genes is actively evolving to adapt to different environments and is acquiring new functions

<b>Table 4.</b> Mapping of <i>cis</i>-elements onto the <i>NCR</i> motifs.

a<p>Elements were mapped onto the five <i>NCR</i> motifs.</p>b<p>Motifs generated by MEME.</p>c<p>Orientation of elements with the <i>NCR</i> motifs on the sense or antisense strands.</p>d<p>E-values of correlation.</p>e<p>Consensus sequence of the elements.</p

Regulatory Patterns of a Large Family of Defensin-Like Genes Expressed in Nodules of <i>Medicago truncatula</i>

<div><p>Root nodules are the symbiotic organ of legumes that house nitrogen-fixing bacteria. Many genes are specifically induced in nodules during the interactions between the host plant and symbiotic rhizobia. Information regarding the regulation of expression for most of these genes is lacking. One of the largest gene families expressed in the nodules of the model legume <i>Medicago truncatula</i> is the nodule cysteine-rich (<i>NCR</i>) group of defensin-like (<i>DEFL</i>) genes. We used a custom Affymetrix microarray to catalog the expression changes of 566 <i>NCR</i>s at different stages of nodule development. Additionally, bacterial mutants were used to understand the importance of the rhizobial partners in induction of <i>NCR</i>s. Expression of early <i>NCR</i>s was detected during the initial infection of rhizobia in nodules and expression continued as nodules became mature. Late <i>NCR</i>s were induced concomitantly with bacteroid development in the nodules. The induction of early and late <i>NCR</i>s was correlated with the number and morphology of rhizobia in the nodule. Conserved 41 to 50 bp motifs identified in the upstream 1,000 bp promoter regions of <i>NCR</i>s were required for promoter activity. These <i>cis</i>-element motifs were found to be unique to the <i>NCR</i> family among all annotated genes in the <i>M. truncatula</i> genome, although they contain sub-regions with clear similarity to known regulatory motifs involved in nodule-specific expression and temporal gene regulation.</p> </div

Expression profiles of <i>NCR</i>s.

<p>Expression values are log₂-transformed intensity values. A, Hierarchical clustering (Euclidian average) of 571 NCR<i>s</i> and 14 treatments. Columns 1, 2, 3, 4, and 5 are data for mock-inoculated roots at 0, 4, 7, 14, and 40 dpi, respectively; columns 6, 7, 10, and 12 are roots inoculated with <i>S. meliloti</i> mutants <i>nodC</i>, <i>exoY</i>, <i>bacA</i> and <i>nifH</i> at 14 dpi, respectively; and columns 8, 9, 11, 13, and 14 are roots inoculated with Sm1021 at 3, 4, 7, 14, and 40 dpi, respectively. Color scales representing signal intensities are shown at the bottom. B, Expression profiles of 346 early <i>NCR</i>s. C, Expression profiles of 79 late <i>NCR</i>s. The box and whisker plots represent five different groups of intensity values, the minimum of which is the lowest whisker, the 25% quartile is represented by the bottom box, the 50% quartile is indicated by the median line, the 75% quartile is represented by the top box, the maximum value is the highest whisker, and the outliers are represented by x’s.</p

<b>Table 3.</b> Over-represented TRANSFAC elements in <i>NCR</i> promoters.

a<p>Element identifier.</p>b<p>TRANSFAC Accession number of the element.</p>c<p>p-values obtained from randomizing the elements using the non-<i>DEFL</i> Mt2.0 genes as background sequence sets. All p-values were 0.0 when using non-nodule <i>DEFL</i>s as a background set.</p

Practical Evaluation and Management of Insomnia in Parkinson's Disease: A Review

ABSTRACT Background Insomnia is one of the most common nonmotor features of Parkinson's disease (PD). However, there are few practical guidelines for providers on how to best evaluate and treat this problem. Methods and Findings This review was developed to provide clinicians with a pragmatic approach to assessing and managing insomnia in PD. Recommendations were based on literature review and expert opinion. We addressed the following topics in this review: prevalence of insomnia in PD, sleep–wake mechanisms, theoretical models of insomnia, risk factors, assessment, pharmacologic and nonpharmacologic treatments. Insomnia treatment choices may be guided by PD severity, comorbidities, and patient preference. However, there is limited evidence supporting pharmacotherapy and nonpharmacologic treatments of insomnia in PD. Conclusions We provide a pragmatic algorithm for evaluating and treating insomnia in PD based on the literature and our clinical experience. We propose personalized insomnia treatment approaches based on age and other issues. Gaps in the existing literature and future directions in the treatment of insomnia in PD are also highlighted