Towards Better Grafting: SCoT and CDDP Analyses for Prediction of the Tomato Rootstocks Performance under Drought Stress

This study aims to predict the behavior of different tomato rootstocks under drought stress conditions. SCoT and CDDP analyses were employed to characterize the genetic relatedness among a commercial drought-sensitive tomato hybrid (cv. Bark) and four wild tomato accessions (LA2711, LA1995, LA3845, and LA4285) known for their tolerance to adverse conditions. The Bark plants were grafted onto the aforementioned wild accessions and self-grafted as control, and then the behavior of all graft unions was followed under normal and drought stress conditions. Our results showed a general genotype-dependent better growth and yield of heterografts than autografts under all growth conditions. Furthermore, clustering analysis based on growth, yield quantity and quality traits, and the leaf content of minerals, ABA, GA3, and proline, in addition to the activity of APX, POD, and DHAR reflected the same grouping pattern of the studied rootstocks exhibited by SCoT and CDDP. The identical grouping pattern supports the utilization of SCoT and CDDP as a robust screening tool helpful to predict the physiological and agronomical behavior of grafting on different tomato rootstocks. Furthermore, grafting could be a cost-efficient alternative method to improve drought tolerance in sensitive tomato genotypes.

Polyploidization Increases the Lipid Content and Improves the Nutritional Quality of Rice

Plant polyploidization is frequently associated with changes in nutrient contents. However, the possible contribution of metabolites to this change has not been investigated by characterizing the metabolite contents of diploid and tetraploid forms of rice (Oryza sativa L.). We compared the metabolites of a group of diploid–tetraploid japonica brown rice and a group of diploid–tetraploid indica brown rice based on liquid chromatography–tandem mass spectrometry. In total, 401 metabolites were identified; of these, between the two diploid–tetraploid groups, 180 showed opposite expression trends, but 221 showed the same trends (147 higher abundance vs. 74 lower abundance). Hierarchical cluster analysis of differential metabolites between diploid and tetraploid species showed a clear grouping pattern, in which the expression abundance of lipids, amino acids and derivatives, and phenolic acids increased in tetraploids. Further analysis revealed that the lipids in tetraploid rice increased significantly, especially unsaturated fatty acids and phospholipids. This study provides further basis for understanding the changes in rice nutritional quality following polyploidization and may serve as a new theoretical reference for breeding eutrophic or functional rice varieties via polyploidization.

Trigger primitive generation algorithm in the CMS barrel muon chambers during HL-LHC

This contribution presents an update on the Analytical Method (AM) algorithm for trigger primitive (TP) generation in the CMS Drift Tube (DT) chambers during the High Luminosity LHC operation (HL-LHC or LHC phase 2). The algorithm has been developed and validated both in software with an emulation approach, and through hardware implementation tests. The algorithm is mainly divided into the following steps: a grouping (pattern recognition) step that finds the path of a given muon, a fitting step to extract the track parameters (position and bending angle), and a correlation step that matches the information from the different super-layers and with signal from the resistive plate chambers. Agreement between the software emulation and the firmware implementation has been verified using different data samples, including a sample of real muons collected during 2016 data taking. In this contribution, an update of the grouping step using a pseudo-Bayes classifier will be discussed.

Variation in morphological characters of Marsilea crenata living in floating aquatic, emergent aquatic, and terrestrial habitats

Wisanti, Aloysius DC, Zubaidah S, Lestari SR. 2021. Variation in morphological characters of Marsilea crenata living in floating aquatic, emergent aquatic, and terrestrial habitats. Biodiversitas 22: 2853-2859. Marsilea is a hydrophyte fern that has plasticity often influenced by enviroment. Several of the species with different habitats or geographies show morphological variations. Therefore, this study aims to analyze the variations in morphological characters of M. crenata growing in aquatic and terrestrial habitats. A total of 38 plant samples were collected from their natural habitats including floating aquatic, emergent aquatic, and terrestrial types. Morphological variations data included 4 qualitative characters and 9 quantitative characters. The quantitative characters were analyzed by one-way ANOVA to test for differences, while the combination of both characters was analyzed using Principal Component Analysis (PCA) to determine the distribution between groups. The data results showed a separate grouping pattern between aquatic and terrestrial populations. These two groups showed significant differences in 5 quantitative characters and 2 qualitative characters. However, emergent aquatic samples’ distribution pattern is closer to the terrestrial group. The characters’ similarity of these two populations was in ??the rhizomes air spaces area, the position between leaflets and absence of red streak on the abaxial lamina. Conclusively, the variations in M. crenata’s morphological characters indicate that this plant has experienced morphological adaptations to water availability in its environment.

Identification of morphometric variation of Aegel marmelos (L.) Correa correlated with habitat types in Western Terai

Aegle marmelos (L.) Correa locally called “Bael” is an economically important plant mainly harvested and traded for medicinal as well as religious purposes. Most of the collection of the plant is from forest. Due to habitat change, deforestation and over harvesting, it is feared that such important plant and its precious genetic diversity may be lost from the nature. Responding to these challenges a major initiative has been launched in the Western Terai Landscape Complex of Nepal to identify morphometric variability in A. marmelos. Morphometric characters variation of this species in Western Terai Landscape Complex was statically and numerically evaluated. Sixteen populations were analysed, using 27 morphological characters of leaves and fruit, collected during 2007/2008 naturally. Most of the morphological characters were not significant with the east-west longitudinal gradient except few were, probably because of small gradient. The variation in the A. marmelos is clearly verified by uni- and multivariate statistics. Highest variation was observed in the (DL) Disc Level (CV= 6.08) from different morphometric characters and later that in PL and B. These DL, PL and B were determining characters of morphometric variation. Similarly, principal component and cluster analysis through forming dendrogram of morphometric traits indicated different grouping pattern of populations. The populations that are nearer to each other are not cluster together. At different sites of sampling analysis of variance in the morphometric traits revealed remarkable variation among population.

Polyploidization Increases the Lipid Content and Improves the Nutritional Quality of Rice

Background: Plant polyploidization is frequently associated with changes in nutrient contents. However, the possible contribution of metabolites to this change has not been investigated by characterizing the metabolite contents of diploid and tetraploid forms of rice ( Oryza sativa L.). Results: We compared the metabolites of a group of diploid–tetraploid japonica brown rice and a group of diploid–tetraploid indica brown rice based on liquid chromatography-tandem mass spectrometry. In total, 401 differential expression metabolites were identified between diploids and tetraploids; of these, between the japonica and indica groups, 180 showed opposite expression trends but 221 showed the same trends (141 up-regulated vs 69 down-regulated). Hierarchical cluster analysis of differential metabolites between diploid and tetraploid species showed a clear grouping pattern, in which the relative contents of lipids, amino acids and derivatives, and phenolic acids increased in tetraploids. Further analysis revealed that the lipids in tetraploid rice increased significantly, especially unsaturated fatty acids and phospholipids. Conclusions: This study provides more basis for the changes in rice nutritional quality following polyploidization, and may serve as a new theoretical reference for breeding eutrophic or functional rice varieties via polyploidization.

Quantitative analysis and mathematic modeling of the global outbreak of COVID-19

The coronavirus pandemic is the biggest in the past 100 years, affected over 200 countries and killed over 300 thousand people. To better understand the epidemics in different areas, the progress percentage was generated in this study by dividing everyday total confirmed case number by the up-to-date total case number, so data obtained from different countries and territories can be put together and compared directly regardless of the large difference in the magnitude of numbers. The global outbreak data were analyzed and categorized into 4 groups based on different epidemic curve stages. The grouping pattern suggests that the geographical position may not play a critical role in the progress of COVID-19 epidemic. In this report, we also used a mathematic model to predict the progress of COVID-19 outbreak in UK, USA and Canada in Group 3, providing valuable information for assessing the risk in these countries and the timing of reopening business.

Whole-Proteome Tree of Arthropods: An “alignment-free” phylogeny of proteome “books”

Background: An “organism tree” of a group of extant-organisms can be considered as a conceptual tree to capture a simplified narrative of the evolutionary course among the organisms. Due to the difficulties of whole-genome sequencing for many organisms, the most common approach has been to construct a “gene tree” by selecting a group of genes common among the organisms, “align” each gene family and estimate evolutionary distances. Despite broad acceptance of the gene trees as the surrogates for the organism trees, there are important limitations and confounding issues with the approach. During last decades, whole-genome sequences of many extant-arthropods became available, providing an opportunity to construct a “whole-proteome tree” of the arthropods, the largest and most species-diverse group of all living animals. Results: An “alignment-free” whole-proteome tree of the arthropods shows that (a) the demographic grouping-pattern is similar to those in the gene trees, but there are notable differences in the branching orders of the groups and the sisterhood relationships between pairs of the groups; and (b) almost all the “founders” of the groups have emerged in an “explosive burst” near the root of the tree. Conclusion: Since the whole-proteome sequence of an organism can be considered as a “book” of amino-acid alphabets, a tree of the books can be constructed, without alignment of sequences, using a text analysis method of Information Theory, which allows comparing the information content of whole-proteomes. Such tree provides another view-point to consider in telling the narrative of kinship among the arthropods.

Whole-Proteome Tree of Insects: An Information-theory-based “alignment-free” phylogeny and grouping of “proteome books”

BackgroundAn “organism tree” of insects, the largest and most species-diverse group of all living animals, can be considered as a metaphorical and conceptual tree to capture a simplified narrative of the complex and unpredictable evolutionary courses of the extant insects. Currently, the most common approach has been to construct a “gene tree”, as a surrogate for the organism tree, by selecting a group of highly alignable regions of each of the select genes/proteins to represent each organism. However, such selected regions account for a small fraction of all genes/proteins and even smaller fraction of whole genome of an organism. During last decades, whole-genome sequences of many extant insects became available, providing an opportunity to construct a “whole-genome or whole-proteome tree” of insects using Information Theory without sequence alignment (alignment-free method).ResultsA whole-proteome tree of the insects shows that (a) the demographic grouping-pattern is similar to those in the gene trees, but there are notable differences in the branching orders of the groups, thus, the sisterhood relationships between pairs of the groups; and (b) all the founders of the major groups have emerged in an “explosive burst” near the root of the tree.ConclusionSince the whole-proteome sequence of an organism can be considered as a “book” of amino-acid alphabets, a tree of the books can be constructed, without alignment of sequences, using a text analysis method of Information Theory. Such tree provides an alternative view-point of constructing a narrative of evolution and kinship among the extant insects.