Investigating hookworm genomes by comparative analysis of two Ancylostoma species

Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics

Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction

The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by incorporation of molecular marker genotypes. However, plant performance or phenotype (P) is determined by the combined effects of genotype (G), envirotype (E), and genotype by environment interaction (GEI). Phenotypes can be predicted more precisely by training a model using data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, and enviromics across time and space). Integration of 3D information profiles (G-P-E), each with multidimensionality, provides predictive breeding with both tremendous opportunities and great challenges. Here, we first review innovative technologies for predictive breeding. We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy, particularly envirotypic data, which have largely been neglected in data collection and are nearly untouched in model construction. We propose a smart breeding scheme, integrated genomic-enviromic prediction (iGEP), as an extension of genomic prediction, using integrated multiomics information, big data technology, and artificial intelligence (mainly focused on machine and deep learning). We discuss how to implement iGEP, including spatiotemporal models, environmental indices, factorial and spatiotemporal structure of plant breeding data, and cross-species prediction. A strategy is then proposed for prediction-based crop redesign at both the macro (individual, population, and species) and micro (gene, metabolism, and network) scales. Finally, we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives. We call for coordinated efforts in smart breeding through iGEP, institutional partnerships, and innovative technological support

Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations

We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integration time step in approaches based on plane-wave expansions. The maximum allowed time step is dictated by the highest frequency components of the fictitious electronic dynamics. These can result either from the large wavevector components of the kinetic energy or from the small wavevector components of the Coulomb potential giving rise to the so called {\it charge sloshing} problem. We show how to eliminate large wavevector instabilities by adopting a preconditioning scheme that is implemented here for the first-time in the context of Car-Parrinello ab-initio molecular dynamics simulations of the ionic motion. We also show how to solve the charge-sloshing problem when this is present. We substantiate our theoretical analysis with numerical tests on a number of different silicon and carbon systems having both insulating and metallic character.Comment: RevTex, 9 figures available upon request, to appear in Phys. Rev.

Anomalous particle-number fluctuations in a three-dimensional interacting Bose-Einstein condensate

The particle-number fluctuations originated from collective excitations are investigated for a three-dimensional, repulsively interacting Bose-Einstein condensate (BEC) confined in a harmonic trap. The contribution due to the quantum depletion of the condensate is calculated and the explicit expression of the coefficient in the formulas denoting the particle-number fluctuations is given. The results show that the particle-number fluctuations of the condensate follow the law $\sim N^{22/15}$ and the fluctuations vanish when temperature approaches to the BEC critical temperature.Comment: RevTex, 4 page

Genomic and transcriptomic analysis identified gene clusters and candidate genes for oil content in peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs

The association between blood metals and hypertension in the GuLF study

Background: Both essential and non-essential metals come from natural and anthropogenic sources. Metals can bioaccumulate in humans and may impact human health, including hypertension. Methods: Blood metal (cadmium, lead, mercury, manganese, and selenium) concentrations were measured at baseline for a sample of participants in the Gulf Long-Term Follow-up (GuLF) Study. The GuLF Study is a prospective cohort study focused on potential health effects following the 2010 Deepwater Horizon oil spill. Hypertension was defined as high systolic (≥140 mm Hg) or diastolic (≥90 mm Hg) blood pressure or taking anti-hypertensive medications. A total of 957 participants who had blood measurement for at least one metal, baseline blood pressure measurements, information on any anti-hypertensive medication use, and relevant covariates were included in this cross-sectional analysis. We used Poisson regression to explore the association between individual blood metal levels and hypertension. Quantile-based g-computation was used to investigate the association between the metal mixture and hypertension. We also explored the association between individual blood metal levels and continuous blood pressure measurements using general linear regression. Results: Comparing the highest quartile of blood metals with the lowest (Q4vs1), the hypertension prevalence ratio (PR) was 0.92 (95 % confidence interval (CI) = 0.73,1.15) for cadmium, 0.86 (95%CI = 0.66,1.12) for lead, 0.89 (95%CI = 0.71,1.12) for mercury, 1.00 (95%CI = 0.80,1.26) for selenium, and 1.22 (95%CI = 0.95,1.57) for manganese. We observed some qualitative differences across race and BMI strata although none of these differences were statistically significant. In stratified analyses, the PR (Q4vs1) for mercury was 0.69 (95%CI = 0.53, 0.91) in White participants and 1.29 (95%CI = 0.86,1.92) in Black participants (p for interaction = 0.5). The PR (Q4vs1) for manganese was relatively higher in Black participants (PR = 1.37, 95%CI = 0.92,2.05) than in White participants (PR = 1.15, 95%CI = 0.83,1.60, p for interaction = 0.5), with a suggestive dose-response among Blacks. After stratifying by obesity (BMI ≥30 and < 30), positive associations of of hypertension with cadmium (PR [Q4vs1] = 1.19, 95%CI = 0.91,1.56, p for interaction = 0.5), lead (PR [Q4vs1] = 1.14, 95%CI = 0.84,1.55, p for interaction = 1.0) and manganese (PR = 1.25, 95%CI = 0.93,1.68, p for interaction = 0.8) were observed in participants with BMI≥30, but not in participants with BMI<30. The joint effect of the metal mixture was 0.96 (95%CI = 0.73,1.27). We did not observe clear associations between blood metal levels and continuous blood pressure measurements. Conclusion: We did not find overall cross-sectional associations between blood cadmium, lead, mercury, selenium levels and hypertension or blood pressure. We found some evidence suggesting that manganese might be positively associated with risk of hypertension. Associations varied somewhat by race and BMI

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future

Kinematical Limits on Higgs Boson Production via Gluon Fusion in Association with Jets

In this paper, we analyze the high-energy limits for Higgs boson plus two jet production. We consider two high-energy limits, corresponding to two different kinematic regions: a) the Higgs boson is centrally located in rapidity between the two jets, and very far from either jet; b) the Higgs boson is close to one jet in rapidity, and both of these are very far from the other jet. In both cases the amplitudes factorize into impact factors or coefficient functions connected by gluons exchanged in the t channel. Accordingly, we compute the coefficient function for the production of a Higgs boson from two off-shell gluons, and the impact factors for the production of a Higgs boson in association with a gluon or a quark jet. We include the full top quark mass dependence and compare this with the result obtained in the large top-mass limit.Comment: 35 pages, 6 figure