Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon

Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs’ amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

A Framework for Automated Scraping of Structured Data Records From the Deep Web Using Semantic Labeling

The intent of this research is to come up with an automated web scraping system which is capable of extracting structured data records embedded in semi-structured web pages. Most of the automated extraction techniques in the literature captures repeated pattern among a set of similarly structured web pages, thereby deducing the template used for the generation of those web pages and then data records extraction is done. All of these techniques exploit computationally intensive operations such as string pattern matching or DOM tree matching and then perform manual labeling of extracted data records. The technique discussed in this paper departs from the state-of-the-art approaches by determining informative sections in the web page through repetition of informative content rather than syntactic structure. From the experiments, it is clear that the system has identified data rich region with 100% precision for web sites belonging to different domains. The experiments conducted on the real world web sites prove the effectiveness and versatility of the proposed approach.

Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs

Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of magnoliids remains poorly understood. By the genome-wide identification of 1,832 NLR genes from seven magnoliid genomes, we built a framework for the evolution of magnoliid R genes. TNL genes were completely absent from five magnoliids, presumably due to immune pathway deficiencies. A total of 74 ancestral R genes (70 CNLs, 3 TNLs, and 1 RNL) were recovered in a common ancestor of magnoliids, from which all current NLR gene repertoires were derived. Tandem duplication served as the major drive for NLR genes expansion in seven magnoliid genomes, as most surveyed angiosperms. Due to recent rapid expansions, most magnoliids exhibited “a first expansion followed by a slight contraction and a further stronger expansion” evolutionary pattern, while both Litsea cubeba and Persea americana showed a two-times-repeated pattern of “expansion followed by contraction.” The transcriptome analysis of seven different tissues of Saururus chinensis revealed a low expression of most NLR genes, with some R genes displaying a relatively higher expression in roots and fruits. Overall, our study sheds light on the evolution of NLR genes in magnoliids, compensates for insufficiency in major angiosperm lineages, and provides an important reference for a better understanding of angiosperm NLR genes.

Two-color super-resolution localization microscopy via joint encoding of emitter location and color

Multi-color super-resolution localization microscopy (SRLM) provides great opportunities for studying the structural and functional details of biological samples. However, current multi-color SRLM methods either suffer from medium to high crosstalk, or require a dedicated optical system and a complicated image analysis procedure. To address these problems, here we propose a completely different method to realize multi-color SRLM. This method is built upon a customized RGBW camera with a repeated pattern of filtered (Red, Green, Blue and Near-infrared) and unfiltered (White) pixels. With a new insight that RGBW camera is advantageous for color recognition instead of color reproduction, we developed a joint encoding scheme of emitter location and color. By combing this RGBW camera with the joint encoding scheme and a simple optical set-up, we demonstrated two-color SRLM with ∼20 nm resolution and < 2% crosstalk (which is comparable to the best reported values). This study significantly reduces the complexity of two-color SRLM (and potentially multi-color SRLM), and thus offers good opportunities for general biomedical research laboratories to use multi-color SRLM, which is currently mastered only by well-trained researchers.

Continuum modeling and vibration analysis of cable-harnessed plate structures of periodic patterns

Over the past decade, modeling of cable-harnessed space structures has received special attention due to the need for better accuracies than the existing models. As these structures become more lightweight upon the advancements in the materials science it is imperative to further consider accurate models in which the dynamic effects of the added cables are better accounted for. Researchers have heavily focused on creating models for cable-harnessed beam-like structures, while very few works have considered plate-like structures. The proposed research aims at the development of an analytical model for cable-harnessed plate-like structures. Cables are assumed to be periodic in geometry to allow for the application of an energy-equivalent homogenization technique. To begin with, a linear displacement field and a second-order Green-Lagrange strain tensor for strain-displacement relationships are considered. The strain and kinetic energies of the fundamental element are found using these relations. The repeated pattern of the fundamental element over the area of the plate structure allows for the employment of the homogenization approach in which the kinetic and strain energies per area of the fundamental element are found and assumed to remain the same as an equivalent homogenized solid plate-like element. The governing dynamic Partial Differential Equations (PDEs) are found using the Hamilton&#x92;s principle. The results are validated using finite element analysis. A detailed parametric analysis is also performed to investigate the effects of various cable parameters and wrapping patterns on the dynamics of the host structure.

A release from developmental bias accelerates morphological diversification in butterfly eyespots

Development can bias the independent evolution of traits sharing ontogenetic pathways, making certain evolutionary changes less likely. The eyespots commonly found on butterfly wings each have concentric rings of differing colors, and these serially repeated pattern elements have been a focus for evo–devo research. In the butterfly family Nymphalidae, eyespots have been shown to function in startling or deflecting predators and to be involved in sexual selection. Previous work on a model species of Mycalesina butterfly,Bicyclus anynana, has provided insights into the developmental control of the size and color composition of individual eyespots. Experimental evolution has also shown that the relative size of a pair of eyespots on the same wing surface is highly flexible, whereas they are resistant to diverging in color composition, presumably due to the underlying shared developmental process. This fixed color composition has been considered as a prime example of developmental bias with significant consequences for wing pattern evolution. Here, we test this proposal by surveying eyespots across the whole subtribe of Mycalesina butterflies and demonstrate that developmental bias shapes evolutionary diversification except in the genusHeteropsiswhich has gained independent control of eyespot color composition. Experimental manipulations of pupal wings reveal that the bias has been released through a novel regional response of the wing tissue to a conserved patterning signal. Our study demonstrates that development can bias the evolutionary independence of traits, but it also shows how bias can be released through developmental innovations, thus, allowing rapid morphological change, facilitating evolutionary diversification.

Myth and philosophy: The Great Sinner’s topos in Ovid, Lucretius and Seneca

In my paper I examine the occurrence of a repeated pattern, namely the catalogue of the so-called Great Sinners, in the work of three Latin authors: Ovid, Lucretius and Seneca. Through the hermeneutical category of (external) intertextuality, the paper explores how the same Leitmotiv is profitably employed by different authors across diverse genres and contexts, changing certain features while retaining the same core. Specifically, it will be shown that these Latin writers drew the list of the Great Sinners from previous sources, but that they also adapted the catalogue to the content and patterns of their own works. Finally, it is noted that these three occurrences of the catalogue should be seen more generally as a specimen for the process of imitatio/aemulatio of previous traditions brought forth by classical writers.

A release from developmental bias accelerates morphological diversification in butterfly eyespots

Development can bias the independent evolution of traits sharing ontogenetic pathways, making certain evolutionary changes less likely. The eyespots commonly found on butterfly wings each have concentric rings of differing colors and these serially repeated pattern elements have been a focus for evo-devo research. In the butterfly family Nymphalidae, eyespots have been shown to function in startling or deflecting predators, and to be involved in sexual selection. Previous work on a model species of Mycalesina butterfly, Bicyclus anynana, has provided insights into the developmental control of the size and color composition of individual eyespots. Experimental evolution has also shown that the relative size of a pair of eyespots on the same wing surface is highly flexible, whereas they are resistant to diverging in color-composition, presumably due to the underlying shared developmental process. This fixed color-composition has been considered as a prime example of developmental bias with significant consequences for wing pattern evolution. Here we test this proposal by surveying eyespots across the whole subtribe of Mycalesina butterflies and demonstrate that developmental bias shapes evolutionary diversification, except in the genus Heteropsis which has gained independent control of eyespot color-composition. Experimental manipulations of pupal wings reveal that the bias has been released through a novel regional response of the wing tissue to a conserved patterning signal. Our study demonstrates that development can bias the evolutionary independence of traits, but it also shows how bias can be released through developmental innovations, thus allowing rapid morphological change, facilitating evolutionary diversification.