Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.

Computer vision meets microfluidics: a label-free method for high-throughput cell analysis

In this paper, we review the integration of microfluidic chips and computer vision, which has great potential to advance research in the life sciences and biology, particularly in the analysis of cell imaging data. Microfluidic chips enable the generation of large amounts of visual data at the single-cell level, while computer vision techniques can rapidly process and analyze these data to extract valuable information about cellular health and function. One of the key advantages of this integrative approach is that it allows for noninvasive and low-damage cellular characterization, which is important for studying delicate or fragile microbial cells. The use of microfluidic chips provides a highly controlled environment for cell growth and manipulation, minimizes experimental variability and improves the accuracy of data analysis. Computer vision can be used to recognize and analyze target species within heterogeneous microbial populations, which is important for understanding the physiological status of cells in complex biological systems. As hardware and artificial intelligence algorithms continue to improve, computer vision is expected to become an increasingly powerful tool for in situ cell analysis. The use of microelectromechanical devices in combination with microfluidic chips and computer vision could enable the development of label-free, automatic, low-cost, and fast cellular information recognition and the high-throughput analysis of cellular responses to different compounds, for broad applications in fields such as drug discovery, diagnostics, and personalized medicine.

Halogen hydrogen-bonded organic framework (XHOF) constructed by singlet open-shell diradical for efficient photoreduction of U(VI)

Synthesis of framework materials possessing specific spatial structures or containing functional ligands has attracted tremendous attention. Herein, a halogen hydrogen-bonded organic framework (XHOF) is fabricated by using Cl- ions as central connection nodes to connect organic ligands, 7,7,8,8-tetraaminoquinodimethane (TAQ), by forming a Cl-···H3 hydrogen bond structure. Unlike metallic node-linked MOFs, covalent bond-linked COFs, and intermolecular hydrogen bond-linked HOFs, XHOFs represent a different kind of crystalline framework. The electron-withdrawing effect of Cl- combined with the electron-rich property of the organic ligand TAQ strengthens the hydrogen bonds and endows XHOF-TAQ with high stability. Due to the production of excited electrons by TAQ under light irradiation, XHOF-TAQ can efficiently catalyze the reduction of soluble U(VI) to insoluble U(IV) with a capacity of 1708 mg-U g-1-material. This study fabricates a material for uranium immobilization for the sustainability of the environment and opens up a new direction for synthesizing crystalline framework materials.

Na+-H+ exchanger 1 determines atherosclerotic lesion acidification and promotes atherogenesis

The pH in atherosclerotic lesions varies between individuals. IgE activates macrophage Na+-H+ exchanger (Nhe1) and induces extracellular acidification and cell apoptosis. Here, we show that the pH-sensitive pHrodo probe localizes the acidic regions in atherosclerotic lesions to macrophages, IgE, and cell apoptosis. In Apoe-/- mice, Nhe1-deficiency or anti-IgE antibody reduces atherosclerosis and blocks lesion acidification. Reduced atherosclerosis in Apoe-/- mice receiving bone marrow from Nhe1- or IgE receptor FcεR1-deficient mice, blunted foam cell formation and signaling in IgE-activated macrophages from Nhe1-deficient mice, immunocomplex formation of Nhe1 and FcεR1 in IgE-activated macrophages, and Nhe1-FcεR1 colocalization in atherosclerotic lesion macrophages support a role of IgE-mediated macrophage Nhe1 activation in atherosclerosis. Intravenous administration of a near-infrared fluorescent pH-sensitive probe LS662, followed by coregistered fluorescent molecular tomography-computed tomography imaging, identifies acidic regions in atherosclerotic lesions in live mice, ushering a non-invasive and radiation-free imaging approach to monitor atherosclerotic lesions in live subjects.