Bourns College of Engineering

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

In evaluating an algorithm, worst-case analysis can be overly pessimistic. Average-case analysis can be overly optimistic. An intermediate approach shows that an algorithm does well on a broad class of input distributions. E. Koutsoupias and C. H. Papadimitriou (1994, in "Proc. of the 35th IEEE Annual Symp. on Foundation of Computer Science," pp. 394-400, IEEE Press, New York) recently analyzed the least-recently-used (LRU) paging strategy in this manner, analyzing its performance on an input sequence generated by a so-called diffuse adversary - one that must choose each request probabilistically so that no page is chosen with probability more than some fixed ∈ > 0. They showed that LRU achieves the optimal competitive ratio (for deterministic on-line algorithms), but they did not determine the actual ratio. In this paper we estimate the optimal ratios within roughly a factor of two for both deterministic strategies and randomized strategies. Around the threshold ∈ ≈ 1/k (where k is the cache size), the optimal ratios are both Θ(In k). Below the threshold the ratios tend rapidly to O(1). Above the threshold the ratio is unchanged for randomized strategies but tends rapidly to Θ(k) for deterministic ones. We also show that the competitive ratios for First-in-first-out (FIFO) and Flush-when-full (FWF) are both k when ∈ ≥ 1/k. In contrast, the ratio for LRU is less than 2 In k + 4 when ∈ = 1/k. It is folklore that LRU outperforms FIFO in practice, but to date the only other variant of competitive analysis in which LRU has been shown to outperform FIFO is the access graph model. For completeness, we give an alternate proof of the optimality of LRU. © 2000 Academic Press.

CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, multi-microsecond molecular dynamics is combined with solution NMR and graph theory-derived models to probe the allosteric role of key specificity-enhancing mutations. We show that mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the allosteric connectivity of the HNH domain, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric communication. This differential perturbation of the allosteric signal correlates to the order of specificity enhancement (K855A > K848A ~ K810A) observed in biochemical studies, with the mutation achieving the highest specificity most strongly perturbing the signaling transfer. These findings suggest that alterations of the allosteric communication from DNA recognition to cleavage are critical to increasing the specificity of Cas9 and that allosteric hotspots can be targeted through mutational studies for improving the system's function.

One major approach to modeling dispersion of pollutants inside confined spaces describes the turbulent transport of material as the product of an eddy diffusivity and the local concentration gradient. This paper examines the applicability of this eddy diffusivity/gradient model by (1) describing the conditions under which this approach is an appropriate representation of turbulent transport, and (2) re-analysis of data provided in studies that have successfully applied gradient transport to describe tracer concentrations. We find that the solutions of the mass conservation equation based on gradient transport provide adequate descriptions of concentration measurements from two studies representative of two types of sources: instantaneous and continuous release of aerosols. We then provide the rationale for the empirical success of the gradient transport model. The solutions of the gradient transport model allow us to examine the relationship between the ventilation rate and the spatial and temporal behavior of the dose of material associated with aerosol releases in a room. We conclude with the associated implications on mitigation of exposure to aerosols such as airborne virus or bacteria.

A thiophene-based tripodal copper(II) complex has been synthesized as a new colorimetric and optical chemosensor for naked-eye discrimination of halides in acetonitrile and an acetonitrile-water mixture. The binding interactions of the new receptor with several anions were analyzed by UV-Vis titrations, electrospray ionization mass spectrometric (ESI-MS) experiments and density functional theory (DFT) calculations. The results from UV-Vis titrations indicate that the coordinative unsaturated copper(II) complex strongly binds a halide at its vacant copper(II) centre via a metal-ligand bond forming a 1:1 complex, exhibiting binding affinities in the order of fluoride > chloride > bromide > iodide. The interactions of the receptor with halides were further confirmed by ESI-MS, showing a distinct signal corresponding to a 1:1 complex for each halide, suggesting that the noncovalent interactions also exist in the gas phase. In addition, time-dependent DFT (TD-DFT) calculations were also carried out to understand the excited-state properties of the chemosensor complexes. A detailed analysis of the TD-DFT calculations shows a consistent red-shift in the first optically-allowed transition, consistent with the observed colorimetric experiments.

Linker-free magnetite nanoparticles (Fe3O4NPs)-decorated gold nanoparticles (AuNPs) were grown using a new protocol that can be used as a new platform for synthesis of other intact metal-metal oxide nanocomposites without the need for linkers. This minimizes the distance between the metal and metal oxide nanoparticles and ensures the optimum combined effects between the two material interfaces. X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy confirmed the successful synthesis of the Fe3O4-Au nanocomposite, without any change in the magnetite phase. Characterization, using transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy, revealed the composite to consist of AuNPs of 70 ± 10 nm diameter decorated with tiny 10 ± 3 nm diameter Fe3O4NPs in Au:Fe mass ratio of 5:1. The prepared Fe3O4-Au nanocomposite was embedded in ionic liquid (IL) and applied for the modification of glassy carbon electrode (GCE) for the electrochemical detection of As(III) in water. By combining the excellent catalytic properties of the AuNPs with the high adsorption capacity of the tiny Fe3O4NPs towards As(III), as well as the good conductivity of IL, the Fe3O4-Au-IL nanocomposite showed excellent performance in the square wave anodic stripping voltammetry detection of As(III). Under the optimized conditions, a linear range of 1 to 100 μg/L was achieved with a detection limit of 0.22 μg/L (S/N = 3), and no interference from 100-fold higher concentrations of a wide variety of cations and anions found in water. A very low residual standard deviation of 1.16% confirmed the high precision/reproducibility of As(III) analysis and the reliability of the Fe3O4-Au-IL sensing interface. Finally, this proposed sensing interface was successfully applied to analyzing synthetic river and wastewater samples with a 95-101% recovery, demonstrating excellent accuracy, even in complex synthetic river and wastewater samples containing high concentrations of humic acid without any sample pretreatments.

This article provides Abaqus input files and user subroutines for performing finite element simulations of the tricuspid heart valve with an idealized geometry. Additional post-processing steps to obtain a ParaView visualization file (*.vtk) of the deformed geometry are also provided to allow the readers to use the included ParaView state file (*.pvsm) for customizable visualization and evaluation of the simulation results. We expect this first-of-its-kind in-silico benchmark dataset will facilitate user-friendly simulations considering material nonlinearity, leaflet-to-leaflet contact, and large deformations. Additionally, the information included herein can be used to rapidly evaluate other novel in-silico approaches developed for simulating cardiac valve function. The benchmark can be expanded to consider more complex features of the tricuspid valve function, such as the dynamic annulus motion or the time-varying transvalvular pressure. Interested readers are referred to the companion article (Johnson et al., 2021) for an example application of this in-silico tool for isogeometric analysis of tricuspid valves.

The emergence and spread of drug-recalcitrant Plasmodium falciparum parasites threaten to reverse the gains made in the fight against malaria. Urgent measures need to be taken to curb this impending challenge. The higher plant-derived sesquiterpene, quinoline alkaloids, and naphthoquinone natural product classes of compounds have previously served as phenomenal chemical scaffolds from which integral antimalarial drugs were developed. Historical successes serve as an inspiration for the continued investigation of plant-derived natural products compounds in search of novel molecular templates from which new antimalarial drugs could be developed. The aim of this study was to identify potential chemical scaffolds for malaria drug discovery following analysis of historical data on phytochemicals screened in vitro against P. falciparum. To identify these novel scaffolds, we queried an in-house manually curated database of plant-derived natural product compounds and their in vitro biological data. Natural products were assigned to different structural classes using NPClassifier. To identify the most promising chemical scaffolds, we then correlated natural compound class with bioactivity and other data, namely (i) potency, (ii) resistance index, (iii) selectivity index and (iv) physicochemical properties. We used an unbiased scoring system to rank the different natural product classes based on the assessment of their bioactivity data. From this analysis we identified the top-ranked natural product pathway as the alkaloids. The top three ranked super classes identified were (i) pseudoalkaloids, (ii) naphthalenes and (iii) tyrosine alkaloids and the top five ranked classes (i) quassinoids (of super class triterpenoids), (ii) steroidal alkaloids (of super class pseudoalkaloids) (iii) cycloeudesmane sesquiterpenoids (of super class triterpenoids) (iv) isoquinoline alkaloids (of super class tyrosine alkaloids) and (v) naphthoquinones (of super class naphthalenes). Launched chemical space of these identified classes of compounds was, by and large, distinct from that of legacy antimalarial drugs. Our study was able to identify chemical scaffolds with acceptable biological properties that are structurally different from current and previously used antimalarial drugs. These molecules have the potential to be developed into new antimalarial drugs.