A Facile Label-Free Colorimetric Assay for DNase I Activity Based on the Peroxidase-Like Activity of Functional Nucleic Acids.

DNase I plays a crucial role in fundamental biological processes, including gene expression, DNA repair, and apoptosis. Therefore, it is important to develop a simple and efficient method to detect DNase I activity. In this work, a colorimetric assay based on functional nucleic acid for sensitive DNase I detection was reported.

A convenient colorimetric assay for Cr(VI) detection based on homogeneous Cu(II)-GMP system with oxidoreductase-like activity.

Hexavalent chromium (Cr(VI)) is an environmental pollutant and recognized as a human carcinogen. Therefore, it is necessary to develop a simple and sensitive detection technique for Cr(VI). Herein, it is found that Cu interacts with guanosine 5'-monophosphate (GMP) to form a homogeneous Cu(II)-GMP complex (Cu·GMP) that efficiently displays the oxidoreductase-like catalytic activity.

Biosynthesis of Epipyrone A Reveals a Highly Specific Membrane-Bound Fungal -Glycosyltransferase for Pyrone Galactosylation.

Epipyrone A is a unique -galactosylated 4-hydroxy-2-pyrone derivative with an antifungal potential from the fungus . We elucidated its biosynthesis via heterologous expression and characterized an unprecedented membrane-bound pyrone -glycosyltransferase biochemically. Molecular docking and mutagenesis experiments suggested a possible mechanism for the heterocyclic -glycosylation and the importance of a transmembrane helix for its catalysis.

KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.

It is difficult to exhaustively screen all possible DNA binding sequences for a given transcription factor (TF). Here, we developed the KaScape method, in which TFs bind to all possible DNA sequences in the same DNA pool where DNA sequences are prepared by randomized oligo synthesis and the random length can be adjusted to a length such as 4, 5, 6, or 7. After separating bound from unbound double-stranded DNAs (dsDNAs), their sequences are determined by next-generation sequencing.

Plant-on-chip: Core morphogenesis processes in the tiny plant .

A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack of synchrony impedes efforts to describe core principles of plant morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use the minimalist known angiosperm to overcome this challenge and provide a model system for plant morphogenesis.

Aptamer-based nanointerferometer enables amplification-free ultrasensitive detection and differentiation of SARS-CoV-2 variants.

The state-of-the-art SARS-CoV-2 detection methods include qRT-PCR and antibody-based lateral flow assay (LFA) point-of-care tests. Despite the high sensitivity and selectivity, qRT-PCR is slow, expensive and needs well-trained operators. On the other extreme, LFA suffers from low sensitivity albeit its fast detection speed, low detection cost and ease of use.

A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data.

Single-cell RNA sequencing is the reference technology to characterize the composition of the tumor microenvironment and to study tumor heterogeneity at high resolution. Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single-cell RNA-seq data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints.

Co-evolution-based prediction of metal-binding sites in proteomes by machine learning.

Metal ions have various important biological roles in proteins, including structural maintenance, molecular recognition and catalysis. Previous methods of predicting metal-binding sites in proteomes were based on either sequence or structural motifs. Here we developed a co-evolution-based pipeline named 'MetalNet' to systematically predict metal-binding sites in proteomes.

DNA-TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families.

Plant-specific TCP transcription factors are key regulators of diverse plant functions. TCP transcription factors have long been annotated as basic helix-loop-helix (bHLH) transcription factors according to remote sequence homology without experimental validation, and their consensus DNA-binding sequences and protein-DNA recognition mechanisms have remained elusive. Here, we report the crystal structures of the class I TCP domain from AtTCP15 and the class II TCP domain from AtTCP10 in complex with different double-stranded DNA (dsDNA).

Human antibody BD-218 has broad neutralizing activity against concerning variants of SARS-CoV-2.

As SARS-CoV-2 variants of concern (VOC) reduce the effectiveness of existing anti-COVID therapeutics, it is increasingly critical to identify highly potent neutralizing antibodies (nAbs) that bind to conserved regions across multiple variants, especially beta, delta, and omicron variants. Using single-cell sequencing with biochemical methods and pseudo-typed virus neutralization experiments, here we report the characterization of a potent nAb BD-218, identified from an early screen of patients recovering from the original virus. We have determined the cryo-EM structure of the BD-218/spike protein complex to define its epitope in detail, which revealed that BD-218 interacts with a novel epitope on the receptor-binding domain (RBD) of the spike protein.

Illuminating the dark protein-protein interactome.

In living systems, a complex network of protein-protein interactions (PPIs) underlies most biochemical events. The human protein-protein interactome has been surveyed using yeast two-hybrid (Y2H)- and mass spectrometry (MS)-based approaches such as affinity purification coupled to MS (AP-MS). Despite decades of systematic investigations and collaborative multi-disciplinary efforts, there is no "gold standard" for documenting PPIs.

Arabidopsis transcription factor TCP4 represses chlorophyll biosynthesis to prevent petal greening.

Green petals pose a challenge for pollinators to distinguish flowers from leaves, but they are valuable as a specialty flower trait. However, little is understood about the molecular mechanisms that underlie the development of green petals. Here, we report that CINCINNATA (CIN)-like TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) proteins play key roles in the control of petal color.

Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor.

The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic.

Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Angiotensin-converting enzyme 2 (ACE2) has been identified as the host cell receptor that binds to the receptor-binding domain (RBD) of the SARS-COV-2 spike protein and mediates cell entry. Because the ACE2 proteins are widely available in mammals, it is important to investigate the interactions between the RBD and the ACE2 of other mammals.

An Approach to Accelerate Healing and Shorten the Hospital Stay of Patients With Anastomotic Leakage After Esophagectomy: An Explorative Study of Systematic Endoscopic Intervention.

Objective: To explore the comprehensive role of systemic endoscopic intervention in healing esophageal anastomotic leak.

Methods: In total, 3919 consecutive patients with esophageal cancer who underwent esophagectomy and immediate esophageal reconstruction were screened. In total, 203 patients (5.

Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.

Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations.

Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities.

The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and therapeutic vulnerabilities. A computational approach for unbiased identification of core biological traits of single cells and bulk tumors uncovered four tumor cell states and GBM subtypes distributed along neurodevelopmental and metabolic axes, classified as proliferative/progenitor, neuronal, mitochondrial and glycolytic/plurimetabolic. Each subtype was enriched with biologically coherent multiomic features.

A map of tumor-host interactions in glioma at single-cell resolution.

Background: Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets.

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.

Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.

Mn Directly Activates cGAS and Structural Analysis Suggests Mn Induces a Noncanonical Catalytic Synthesis of 2'3'-cGAMP.

DNA binding allosterically activates the cytosolic DNA sensor cGAS (cyclic GMP-AMP [cGAMP] synthase) to synthesize 2'3'-cGAMP, using Mg as the metal cofactor that catalyzes two nucleotidyl-transferring reactions. We previously found that Mn potentiates cGAS activation, but the underlying mechanism remains unclear. Here, we report that Mn directly activates cGAS.

Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies.

Brain tumors are among the most challenging human tumors for which the mechanisms driving progression and heterogeneity remain poorly understood. We combined single-cell RNA-seq with multi-sector biopsies to sample and analyze single-cell expression profiles of gliomas from 13 Chinese patients. After classifying individual cells, we generated a spatial and temporal landscape of glioma that revealed the patterns of invasion between the different sub-regions of gliomas.

Parkinson's disease associated mutation E46K of α-synuclein triggers the formation of a distinct fibril structure.

Amyloid aggregation of α-synuclein (α-syn) is closely associated with Parkinson's disease (PD) and other synucleinopathies. Several single amino-acid mutations (e.g.