Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2's preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate

(E)-N′-(2-Chloro­benzyl­idene)-3,5-di­hydroxy­benzohydrazide dihydrate

In the Schiff base mol­ecule of the title compound, C14H11ClN2O3·2H2O, the benzene rings form a dihedral angle of 20.6 (1)°. The water molecules of crystallization are involved in the formation of a three-dimensional hydrogen-bonding network via O—H⋯O and N—H⋯O hydrogen bonds

Effects of Gualou Guizhi Decoction Aqueous Extract on Axonal Regeneration in Organotypic Cortical Slice Culture after Oxygen-Glucose Deprivation

Gualou Guizhi decoction (GLGZD) is effective for the clinical treatment of limb spasms caused by ischemic stroke, but its underlying mechanism is unclear. Propidium iodide (PI) fluorescence staining, terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL), immunohistochemistry, western blot, and real-time qPCR were used to observe the axonal regeneration and neuroprotective effects of GLGZD aqueous extract on organotypic cortical slices exposed to oxygen-glucose deprivation (OGD) and further elucidate the potential mechanisms. Compared with the OGD group, the GLGZD aqueous extract decreased the red PI fluorescence intensity; inhibited neuronal apoptosis; improved the growth of slice axons; upregulated the protein expression of tau and growth-associated protein-43; and decreased protein and mRNA expression of neurite outgrowth inhibitor protein-A (Nogo-A), Nogo receptor 1 (NgR1), ras homolog gene family A (RhoA), rho-associated coiled-coil-containing protein kinase (ROCK), and phosphorylation of collapsin response mediator protein 2 (CRMP2). Our study found that GLGZD had a strong neuroprotective effect on brain slices after OGD injury. GLGZD plays a vital role in promoting axonal remodeling and functional remodeling, which may be related to regulation of the expression of Nogo-A and its receptor NgR1, near the injured axons, inhibition of the Rho-ROCK pathway, and reduction of CRMP2 phosphorylation

Brainformers: Trading Simplicity for Efficiency

Transformers are central to recent successes in natural language processing and computer vision. Transformers have a mostly uniform backbone where layers alternate between feed-forward and self-attention in order to build a deep network. Here we investigate this design choice and find that more complex blocks that have different permutations of layer primitives can be more efficient. Using this insight, we develop a complex block, named Brainformer, that consists of a diverse sets of layers such as sparsely gated feed-forward layers, dense feed-forward layers, attention layers, and various forms of layer normalization and activation functions. Brainformer consistently outperforms the state-of-the-art dense and sparse Transformers, in terms of both quality and efficiency. A Brainformer model with 8 billion activated parameters per token demonstrates 2x faster training convergence and 5x faster step time compared to its GLaM counterpart. In downstream task evaluation, Brainformer also demonstrates a 3% higher SuperGLUE score with fine-tuning compared to GLaM with a similar number of activated parameters. Finally, Brainformer largely outperforms a Primer dense model derived with NAS with similar computation per token on fewshot evaluations

Human Leukocyte Antigen Typing Using a Knowledge Base Coupled with a High-Throughput Oligonucleotide Probe Array Analysis

Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world’s populations, benefiting both global public health and personalized health care

All‐In‐One OsciDrop Digital PCR System for Automated and Highly Multiplexed Molecular Diagnostics

Digital PCR (dPCR) holds immense potential for precisely detecting nucleic acid markers essential for personalized medicine. However, its broader application is hindered by high consumable costs, complex procedures, and restricted multiplexing capabilities. To address these challenges, an all‐in‐one dPCR system is introduced that eliminates the need for microfabricated chips, offering fully automated operations and enhanced multiplexing capabilities. Using this innovative oscillation‐induced droplet generation technique, OsciDrop, this system supports a comprehensive dPCR workflow, including precise liquid handling, pipette‐based droplet printing, in situ thermocycling, multicolor fluorescence imaging, and machine learning‐driven analysis. The system's reliability is demonstrated by quantifying reference materials and evaluating HER2 copy number variation in breast cancer. Its multiplexing capability is showcased with a quadruplex dPCR assay that detects key EGFR mutations, including 19Del, L858R, and T790M in lung cancer. Moreover, the digital stepwise melting analysis (dSMA) technique is introduced, enabling high‐multiplex profiling of seven major EGFR variants spanning 35 subtypes. This innovative dPCR system presents a cost‐effective and versatile alternative, overcoming existing limitations and paving the way for transformative advances in precision diagnostics

The Fabrication of Nano-Particles in Aqueous Solution From Oxyfluoride Glass Ceramics by Thermal Induction and Corrosion Treatment

An innovative route is reported to fabricate nano-particles in aqueous solution from oxyfluoride glass by the thermal induction and corrosion treatment in this letter. The investigations of X-ray diffraction and transmission electron microscope based on nano-particles in glass ceramics (GCs) and aqueous solution indicate that the nano-particles formed in glass matrix during the thermal induction process are released to aqueous solution and their structure, shape and luminescent properties in glass host can be kept. Owing to the designable composition of the nano-particles during glass preparation process, the method is a novel way to obtain nano-particles in aqueous solution from GCs