Editorial: Protecting Our Crops - Approaches for Plant Parasitic Nematode Control

In agricultural history, the Green Revolution generated by the development of breeding technology, chemical fertilizers, and pesticides has enabled mass production of agricultural crops and solved many (but not all) hunger problems around the world (Pingali, 2012). Plants make up about 80% of the food we consume, while about 40% of food crops are lost by agricultural pests, including plant nematodes (FAO, 2019). The world population in 2021 is  7.8 billion and is estimated to reach 10 billion in 2050 (United Nations, 2019). The current proposition imposed on us is to develop methods to increase crop yield and quality while suppressing damage from pests and also reducing the impact on the natural environment. Plant-parasitic nematodes (PPNs) are one of the major constraints in agriculture. Damage caused by PPNs has been estimated from $US80 billion (Nicol et al., 2011) to$US157 billion per year (Abad et al., 2008). However, the full extent of nematode damage is likely underestimated as many growers, particularly in developing countries, are unaware of the presence of PPNs (Jones et al., 2013). This was assumed as nematodes are usually small-body-size, soil-borne pathogens, and the symptoms they cause are often non-specific (Jones et al., 2013). The damage caused by PPNs could be even worse in the future in the context of a growing world population under a Climate Change scenario and the removal or reduction in the use of some nematicides in many parts of the world. Set in the context of the 2020 International Year of Plant Health, this Research Topic “Protecting Our Crops - Approaches for Plant Parasitic Nematode Control” gives new insights into Integrative Approaches for Sustainable PPN Control. Many of the articles are excellent reviews of their specific topic, which could help in pointing out new research directions

Temperature dependence in interatomic potentials and an improved potential for Ti

The process of deriving an interatomic potentials represents an attempt to integrate out the electronic degrees of freedom from the full quantum description of a condensed matter system. In practice it is the derivatives of the interatomic potentials which are used in molecular dynamics, as a model for the forces on a system. These forces should be the derivative of the free energy of the electronic system, which includes contributions from the entropy of the electronic states. This free energy is weakly temperature dependent, and although this can be safely neglected in many cases there are some systems where the electronic entropy plays a significant role. Here a method is proposed to incorporate electronic entropy in the Sommerfeld approximation into empirical potentials. The method is applied as a correction to an existing potential for titanium. Thermal properties of the new model are calculated, and a simple method for fixing the melting point and solid-solid phase transition temperature for existing models fitted to zero temperature data is presented.Comment: CCP 201

Two-dimensional Vortices in Superconductors

Superconductors have two key characteristics. They expel magnetic field and they conduct electrical current with zero resistance. However, both properties are compromised in high magnetic fields which can penetrate the material and create a mixed state of quantized vortices. The vortices move in response to an electrical current dissipating energy which destroys the zero resistance state\cite{And64}. One of the central problems for applications of high temperature superconductivity is the stabilization of vortices to ensure zero electrical resistance. We find that vortices in the anisotropic superconductor Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8+\delta}$ (Bi-2212) have a phase transition from a liquid state, which is inherently unstable, to a two-dimensional vortex solid. We show that at high field the transition temperature is independent of magnetic field, as was predicted theoretically for the melting of an ideal two-dimensional vortex lattice\cite{Fis80,Gla91}. Our results indicate that the stable solid phase can be reached at any field as may be necessary for applications involving superconducting magnets\cite{Has04,Sca04,COHMAG}. The vortex solid is disordered, as suggested by previous studies at lower fields\cite{Lee93,Cub93}. But its evolution with increasing magnetic field displays unexpected threshold behavior that needs further investigation.Comment: 5 pages and 4 figures. submitted to Nature Physic

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance

HIV-Specific Probabilistic Models of Protein Evolution

Comparative sequence analyses, including such fundamental bioinformatics techniques as similarity searching, sequence alignment and phylogenetic inference, have become a mainstay for researchers studying type 1 Human Immunodeficiency Virus (HIV-1) genome structure and evolution. Implicit in comparative analyses is an underlying model of evolution, and the chosen model can significantly affect the results. In general, evolutionary models describe the probabilities of replacing one amino acid character with another over a period of time. Most widely used evolutionary models for protein sequences have been derived from curated alignments of hundreds of proteins, usually based on mammalian genomes. It is unclear to what extent these empirical models are generalizable to a very different organism, such as HIV-1–the most extensively sequenced organism in existence. We developed a maximum likelihood model fitting procedure to a collection of HIV-1 alignments sampled from different viral genes, and inferred two empirical substitution models, suitable for describing between-and within-host evolution. Our procedure pools the information from multiple sequence alignments, and provided software implementation can be run efficiently in parallel on a computer cluster. We describe how the inferred substitution models can be used to generate scoring matrices suitable for alignment and similarity searches. Our models had a consistently superior fit relative to the best existing models and to parameter-rich data-driven models when benchmarked on independent HIV-1 alignments, demonstrating evolutionary biases in amino-acid substitution that are unique to HIV, and that are not captured by the existing models. The scoring matrices derived from the models showed a marked difference from common amino-acid scoring matrices. The use of an appropriate evolutionary model recovered a known viral transmission history, whereas a poorly chosen model introduced phylogenetic error. We argue that our model derivation procedure is immediately applicable to other organisms with extensive sequence data available, such as Hepatitis C and Influenza A viruses

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes

Multiparticle azimuthal correlations for extracting event-by-event elliptic and triangular flow in Au + Au collisions at sNN =200 GeV

We present measurements of elliptic and triangular azimuthal anisotropy of charged particles detected at forward rapidity 1<|η|<3 in Au + Au collisions at sNN=200 GeV, as a function of centrality. The multiparticle cumulant technique is used to obtain the elliptic flow coefficients v2{2},v2{4},v2{6}, and v2{8}, and triangular flow coefficients v3{2} and v3{4}. Using the small-variance limit, we estimate the mean and variance of the event-by-event v2 distribution from v2{2} and v2{4}. In a complementary analysis, we also use a folding procedure to study the distributions of v2 and v3 directly, extracting both the mean and variance. Implications for initial geometrical fluctuations and their translation into the final-state momentum distributions are discussed

Nonperturbative transverse-momentum-dependent effects in dihadron and direct photon-hadron angular correlations in p+p collisions at s =200 GeV

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at s=200 GeV. The correlations are sensitive to nonperturbative initial-state and final-state transverse momenta kT and jT in the azimuthal nearly back-to-back region Δφ∼π. To have sensitivity to small transverse momentum scales, nonperturbative momentum widths of pout, the out-of-plane transverse-momentum component perpendicular to the trigger particle, are measured. In this region, the evolution of pout can be studied when several different hard scales are measured. These widths are used to investigate possible effects from transverse-momentum-dependent factorization breaking. When accounting for the longitudinal-momentum fraction of the away-side hadron with respect to the near-side trigger particle, the widths are found to increase with the hard scale; this is qualitatively similar to the observed behavior in Drell-Yan and semi-inclusive deep-inelastic scattering interactions, where factorization is predicted to hold. The momentum widths are also studied as a function of center-of-mass energy by comparing to previous measurements at s=510 GeV. The nonperturbative jet widths also appear to increase with s at a similar xT, which is qualitatively consistent to similar measurements in Drell-Yan interactions. Future detailed global comparisons between measurements of processes where transverse-momentum-dependent factorization is predicted to hold and be broken will provide further insight into the role of color in hadronic interactions

Nonperturbative-transverse-momentum broadening in dihadron angular correlations in sNN =200 GeV proton-nucleus collisions

The PHENIX collaboration has measured high-pT dihadron correlations in p+p, p+Al, and p+Au collisions at sNN=200 GeV. The correlations arise from inter- and intrajet correlations and thus have sensitivity to nonperturbative effects in both the initial and final states. The distributions of pout, the transverse-momentum component of the associated hadron perpendicular to the trigger hadron, are sensitive to initial- and final-state transverse momenta. These distributions are measured multidifferentially as a function of xE, the longitudinal momentum fraction of the associated hadron with respect to the trigger hadron. The near-side pout widths, sensitive to fragmentation transverse momentum, show no significant broadening between p+Au, p+Al, and p+p. The away-side nonperturbative pout widths are found to be broadened in p+Au when compared to p+p; however, there is no significant broadening in p+Al compared to p+p collisions. The data also suggest that the away-side pout broadening is a function of Ncoll, the number of binary nucleon-nucleon collisions, in the interaction. The potential implications of these results with regard to initial- and final-state transverse-momentum broadening and energy loss of partons in a nucleus, among other nuclear effects, are discussed