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Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence–absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora. 

While salinity can alter the photodegradation of hydrophobic organic compounds (HOCs), the cause of their altered kinetics in seawater is not well understood. Because HOC intermediate photoproducts are often more toxic than their parent compounds, characterizing the generation of intermediates in saline environments is needed to accurately predict their health effects. The present study investigated the influence of salinity on the generation of anthraquinone through the photolysis of anthracene and the generation of anthrone and 1-hydroxyanthraquinone from the photolysis of anthraquinone as well as their reactivities with hydroxyl radicals. This was conducted by measuring the photolysis rates of anthracene and anthraquinone and characterizing their product formation in buffered deionized water, artificial seawater, individual seawater halides (bromide, chloride, and iodide), dimethyl sulfoxide, furfuryl alcohol, and solutions of hydrogen peroxide. Salinity enhanced the persistence of anthraquinone by a factor >10 and altered its product formation, including the generation of the suspected carcinogen 1-hydroxyanthraquinone. In part, this was attributed to reactive oxygen species (ROS) scavenging by the seawater constituents chloride and bromide. In addition, anthraquinone and its hydroxylated products were found to be moderately to highly reactive with hydroxyl radicals, further illustrating their tendency to react with ROS in aqueous environments. The present study emphasizes the importance of considering the effects of salinity on organic contaminant degradation; it can significantly enhance the persistence of HOCs and alter their intermediate formation, subsequently impacting chemical exposure times and potential toxic effects on estuarine/marine organisms. Environ Toxicol Chem 2023;42:1721–1729. © 2023 SETAC.

 

The recurrence of cancer following chemotherapy treatment is a major cause of death across solid and hematologic cancers. In B-cell acute lymphoblastic leukemia (B-ALL), relapse after initial chemotherapy treatment leads to poor patient outcomes. Here we test the hypothesis that chemotherapy-treated versus control B-ALL cells can be characterized based on cellular physical phenotypes. To quantify physical phenotypes of chemotherapy-treated leukemia cells, we use cells derived from B-ALL patients that are treated for 7 days with a standard multidrug chemotherapy regimen of vincristine, dexamethasone, and L-asparaginase (VDL). We conduct physical phenotyping of VDL-treated versus control cells by tracking the sequential deformations of single cells as they flow through a series of micron-scale constrictions in a microfluidic device; we call this method Quantitative Cyclical Deformability Cytometry. Using automated image analysis, we extract time-dependent features of deforming cells including cell size and transit time (TT) with single-cell resolution. Our findings show that VDL-treated B-ALL cells have faster TTs and transit velocity than control cells, indicating that VDL-treated cells are more deformable. We then test how effectively physical phenotypes can predict the presence of VDL-treated cells in mixed populations of VDL-treated and control cells using machine learning approaches. We find that TT measurements across a series of sequential constrictions can enhance the classification accuracy of VDL-treated cells in mixed populations using a variety of classifiers. Our findings suggest the predictive power of cell physical phenotyping as a complementary prognostic tool to detect the presence of cells that survive chemotherapy treatment. Ultimately such complementary physical phenotyping approaches could guide treatment strategies and therapeutic interventions.

Insight box Cancer cells that survive chemotherapy treatment are major contributors to patient relapse, but the ability to predict recurrence remains a challenge. Here we investigate the physical properties of leukemia cells that survive treatment with chemotherapy drugs by deforming individual cells through a series of micron-scale constrictions in a microfluidic channel. Our findings reveal that leukemia cells that survive chemotherapy treatment are more deformable than control cells. We further show that machine learning algorithms applied to physical phenotyping data can predict the presence of cells that survive chemotherapy treatment in a mixed population. Such an integrated approach using physical phenotyping and machine learning could be valuable to guide patient treatments.

 

Electronic spins can form long-range entangled phases of condensed matter named quantum spin liquids. Their existence is conceptualized in models of two- or three-dimensional frustrated magnets that evade symmetry-breaking order down to zero temperature. Quantum spin ice (QSI) is a theoretically well-established example described by an emergent quantum electrodynamics, with excitations behaving like photon and matter quasiparticles. The latter are fractionally charged and equivalent to the `spinons' emerging from coherent phases of singlets in one dimension, where clear experimental proofs of fractionalization exist. However, in frustrated magnets it remains difficult to establish consensual evidence for quantum spin liquid ground states and their fractional excitations. Here, we use backscattering neutron spectroscopy to achieve extremely high resolution of the time-dependent magnetic response of the candidate QSI material Ce2Sn2O7. We find a gapped spectrum featuring a threshold and peaks that match theories for pair production and propagation of fractional matter excitations (spinons) strongly coupled to a background gauge field. The observed peaks provide evidence for a QSI through spectroscopic signatures of space-time symmetry fractionalization, while the threshold behavior corroborates the regime of strong light-matter interaction predicted for the emergent universe in a QSI. 

The emergence of scalar Higgs-type amplitude modes in systems where symmetry is spontaneously broken has been a highly successful, paradigmatic description of phase transitions, with implications ranging from high-energy particle physics to low-energy condensed matter systems. Here, we uncover two successive high temperature phase transitions in the pyrochlore magnet Nd₂Ru₂O₇atT_N = 147 K andT^* = 97 K, that lead to giant phonon instabilities and culminate in the emergence of a highly coherent excitation. This coherent excitation, distinct from other phonons and from conventional magnetic modes, stabilizes at a low energy of 3 meV. We assign it to a collective Higgs-type amplitude mode, that involves bond energy modulations of the Ru₄tetrahedra. Its striking two-fold symmetry, incompatible with the underlying crystal structure, highlights the possibility of multiple entangled broken symmetries.