Single-cell genomic analysis in plants

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis

Franck-Condon Effect in Central Spin System

We study the quantum transitions of a central spin surrounded by a collective-spin environment. It is found that the influence of the environmental spins on the absorption spectrum of the central spin can be explained with the analog of the Franck-Condon (FC) effect in conventional electron-phonon interaction system. Here, the collective spins of the environment behave as the vibrational mode, which makes the electron to be transitioned mainly with the so-called "vertical transitions" in the conventional FC effect. The "vertical transition" for the central spin in the spin environment manifests as, the certain collective spin states of the environment is favored, which corresponds to the minimal change in the average of the total spin angular momentum.Comment: 8 pages, 8 figure

Multipoint efficient iterative methods and the dynamics of Ostrowski's method

This is an Author's Accepted Manuscript of an article published in José L. Hueso, Eulalia Martínez & Carles Teruel (2019) Multipoint efficient iterative methods and the dynamics of Ostrowski's method, International Journal of Computer Mathematics, 96:9, 1687-1701, DOI: 10.1080/00207160.2015.1080354 in the International Journal of Computer Mathematics, SEP 2 2019 [copyright Taylor & Francis], available online at: http://www.tandfonline.com/10.1080/00207160.2015.1080354[EN] In this work, we introduce a modification into the technique, presented in A. Cordero, J.L. Hueso, E. Martinez, and J.R. Torregrosa [Increasing the convergence order of an iterative method for nonlinear systems, Appl. Math. Lett. 25 (2012), pp. 2369-2374], that increases by two units the convergence order of an iterative method. The main idea is to compose a given iterative method of order p with a modification of Newton's method that introduces just one evaluation of the function, obtaining a new method of order p+2, avoiding the need to compute more than one derivative, so we improve the efficiency index in the scalar case. This procedure can be repeated n times, with the same approximation to the derivative, obtaining new iterative methods of order p+2n. We perform different numerical tests that confirm the theoretical results. By applying this procedure to Newton's method one obtains the well known fourth order Ostrowski's method. We finally analyse its dynamical behaviour on second and third degree real polynomials.This research was supported by Ministerio de Economia y Competitividad under grant PGC2018-095896-B-C22 and by the project of Generalitat Valenciana Prometeo/2016/089.Hueso, JL.; Martínez Molada, E.; Teruel-Ferragud, C. (2019). Multipoint efficient iterative methods and the dynamics of Ostrowski's method. International Journal of Computer Mathematics. 96(9):1687-1701. https://doi.org/10.1080/00207160.2015.1080354S16871701969Amat, S., Busquier, S., & Plaza, S. (2010). Chaotic dynamics of a third-order Newton-type method. Journal of Mathematical Analysis and Applications, 366(1), 24-32. doi:10.1016/j.jmaa.2010.01.047Cordero, A., & Torregrosa, J. R. (2007). Variants of Newton’s Method using fifth-order quadrature formulas. Applied Mathematics and Computation, 190(1), 686-698. doi:10.1016/j.amc.2007.01.062Cordero, A., Martínez, E., & Torregrosa, J. R. (2009). Iterative methods of order four and five for systems of nonlinear equations. Journal of Computational and Applied Mathematics, 231(2), 541-551. doi:10.1016/j.cam.2009.04.015Cordero, A., Hueso, J. L., Martínez, E., & Torregrosa, J. R. (2012). Increasing the convergence order of an iterative method for nonlinear systems. Applied Mathematics Letters, 25(12), 2369-2374. doi:10.1016/j.aml.2012.07.005Jarratt, P. (1966). Some fourth order multipoint iterative methods for solving equations. Mathematics of Computation, 20(95), 434-434. doi:10.1090/s0025-5718-66-99924-

Percolation on two- and three-dimensional lattices

In this work we apply a highly efficient Monte Carlo algorithm recently proposed by Newman and Ziff to treat percolation problems. The site and bond percolation are studied on a number of lattices in two and three dimensions. Quite good results for the wrapping probabilities, correlation length critical exponent and critical concentration are obtained for the square, simple cubic, HCP and hexagonal lattices by using relatively small systems. We also confirm the universal aspect of the wrapping probabilities regarding site and bond dilution.Comment: 15 pages, 6 figures, 3 table

Measurement of Trace I-129 Concentrations in CsI Powder and Organic Liquid Scintillator with Accelerator Mass Spectrometry

Levels of trace radiopurity in active detector materials is a subject of major concern in low-background experiments. Procedures were devised to measure trace concentrations of I-129 in the inorganic salt CsI as well as in organic liquid scintillator with Accelerator Mass Spectrometry (AMS) which leads to improvement in sensitivities by several orders of magnitude over other methods. No evidence of their existence in these materials were observed. Limits of < 6 X 10^{-13} g/g and < 2.6 X 10^{-17} g/g on the contaminations of I-129 in CsI and liquid scintillator, respectively, were derived.These are the first results in a research program whose goals are to develop techniques to measure trace radioactivity in detector materials by AMS.Comment: Proceedings of 10th International Conference on Accelerator Mass Spectrometr

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop

Spinor Field in Bianchi type-I Universe: regular solutions

Self-consistent solutions to the nonlinear spinor field equations in General Relativity has been studied for the case of Bianchi type-I (B-I) space-time. It has been shown that, for some special type of nonliearity the model provides regular solution, but this singularity-free solutions are attained at the cost of broken dominant energy condition in Hawking-Penrose theorem. It has also been shown that the introduction of $\Lambda$-term in the Lagrangian generates oscillations of the B-I model, which is not the case in absence of $\Lambda$ term. Moreover, for the linear spinor field, the $\Lambda$ term provides oscillatory solutions, those are regular everywhere, without violating dominant energy condition. Key words: Nonlinear spinor field (NLSF), Bianch type -I model (B-I), $\Lambda$ term PACS 98.80.C CosmologyComment: RevTex, 21 page

Association between first caesarean delivery and adverse outcomes in subsequent pregnancy: a retrospective cohort study

BACKGROUND:Few studies have explored the association between a previous caesarean section (CS) and adverse perinatal outcomes in a subsequent pregnancy, especially in women who underwent a non-indicated CS in their first delivery. We designed this study to compare the perinatal outcomes of a subsequent pregnancy in women who underwent spontaneous vaginal delivery (SVD) or CS in their first delivery. METHODS:This retrospective cohort study included women who underwent singleton deliveries at the International Peace Maternity and Child Health Hospital from January 2013 to December 2016. Data on the perinatal outcomes of all the women were extracted from the medical records. Multivariate logistic regression was conducted to assessed the association between CS in the first delivery and adverse perinatal outcomes in the subsequent pregnancy. RESULTS:CS delivery in the subsequent pregnancy was more likely for women who underwent CS in their first birth than for women with previous SVD (97.3% versus 13.2%). CS in the first birth was also associated with a significantly increased risk of adverse outcomes in the subsequent pregnancy, especially in women who underwent a non-indicated CS. Adverse perinatal outcomes included pregnancy-induced hypertension [adjusted odds ratio (OR), 95% confidence interval (CI): 2.20, 1.59-3.05], gestational diabetes mellitus (1.82, 1.57-2.11), gestational anaemia (1.27, 1.05-1.55), placenta previa (3.18, 2.15-4.71), placenta accreta (2.75, 1.75-4.31), and polyhydramnios (2.60, 1.57-4.31) in the mother and preterm delivery (1.37, 1.06-1.78), low birth weight (3.78, 2.07-6.90), macrosomia (5.04, 3.95-6.44), and neonatal jaundice (1.72, 1.39-2.14) in the baby. CONCLUSIONS:CS in the first delivery markedly increases the risk of repeated CS and maternal-fetal complications in the subsequent pregnancy, especially in women with a non-indicated CS.Hong-Tao Hu, Jing-Jing Xu, Jing Lin, Cheng Li, Yan-Ting Wu, Jian-Zhong Sheng, Xin-Mei Liu and He-Feng Huan

Carleson Measures and Toeplitz Operators

In this last chapter we shall describe an application of the Kobayashi distance to geometric function theory and functional analysis of holomorphic functions