Hemorrhoids and cardiovascular disease: A bidirectional Mendelian randomization study.

Background: Emerging evidence suggests that hemorrhoids are associated with cardiovascular disease (CVD). However, the causal associations between hemorrhoids and CVD remain elusive. This study aimed to investigate potential causal links between hemorrhoids and various heart conditions, including arrhythmia, heart failure, myocardial infarction, atrial fibrillation, and coronary artery disease.

Conversion of IscB and Cas9 into RNA-guided RNA editors.

RNA-guided RNA editing represents an attractive alternative to DNA editing. However, the prevailing tool, CRISPR-Cas13, has collateral RNA cleavage activity that causes undesirable cytotoxicity in human cells. Here, we report an ultracompact RNA-editing platform engineered from IscB, which has comparable or higher activity than Cas13 but without cytotoxicity concerns.

Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown.

Integrases from the "large serine" family are simple, highly directional site-specific DNA recombinases that have great promise as synthetic biology and genome editing tools. Integrative recombination (mimicking phage or mobile element insertion) requires only integrase and two short (∼40-50) DNA sites. The reverse reaction, excisive recombination, does not occur until it is triggered by the presence of a second protein termed a recombination directionality factor (RDF), which binds specifically to its cognate integrase.

High-precision cytosine base editors by evolving nucleic-acid-recognition hotspots in deaminase.

Base editors (BEs), covalent fusions of a cytosine or adenine deaminase with a nuclease-impaired CRISPR protein, mediate site-specific conversion of C:G to T:A (CBEs) or A:T to G:C (ABEs) in the genome. Existing BEs modify all cytosines or adenines within the editing window, which limits their precision. Here we engineer nucleotide and context specificity of the Escherichia coli transfer RNA-specific adenosine deaminase (TadA) to pinpoint cytosine editing.

Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation.

Synonymous mutations, once known as "silent" mutations, are increasingly attracting the interest of biologists. Although they may affect transcriptional or post-transcriptional processes, their impact on biological traits remains under-investigated, particularly at the organismal level. Here, we identified two closely linked, epistatically interacting genes: YTH1, an RNA N-methyladenosine (mA) reader, and ACS2, an aminocyclopropane-1-carboxylic acid (ACC) synthase, which contribute to cucumber fruit length domestication.

Charting the development and engineering of CRISPR base editors: lessons and inspirations.

CRISPR base editors (BEs) have introduced a new chapter in precise genome editing. The brief but fruitful history of BE development documents many case studies that not only lay the foundation of base-editing technology but are also instrumental to future protein engineering efforts. In this review, we summarize the development and engineering of various BEs with a focus on recent progress.

m6A modification is incorporated into bacterial mRNA without specific functional benefit.

N 6-Methyladenosine (m6A), the most abundant modification in eukaryotic messenger RNAs (mRNAs), has also been found at a low level in bacterial mRNAs. However, enzyme(s) that introduce m6A modification on mRNAs in bacteria remain elusive. In this work, we combine deep-sequencing approaches that identify m6A sites with in vitro biochemical studies to identify putative m6A methyltransferases that would modify Escherichia coli mRNAs.

Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.

Protein-RNA interactions govern nearly every aspect of RNA metabolism and are frequently dysregulated in disease. While individual protein residues and RNA nucleotides critical for these interactions have been characterized, scalable methods that jointly map protein- and RNA-level determinants remain limited. RNA deaminase fusions have emerged as a powerful strategy to identify transcriptome-wide targets of RNA-binding proteins by converting binding events into site-specific nucleotide edits.

Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.

Bloodstream infections (BSIs) pose a significant diagnostic challenge, largely due to the limitations of traditional methods such as blood cultures. These methods often yield low positive rates, have lengthy processing times that delay treatment, and are limited in detecting only a narrow range of pathogens. Such delays and inaccuracies can critically impede timely clinical interventions, potentially compromising patient outcomes.

Assessing and engineering the IscB-ωRNA system for programmed genome editing.

OMEGA RNA (ωRNA)-guided endonuclease IscB, the evolutionary ancestor of Cas9, is an attractive system for in vivo genome editing because of its compact size and mechanistic resemblance to Cas9. However, wild-type IscB-ωRNA systems show limited activity in human cells. Here we report enhanced OgeuIscB, which, with eight amino acid substitutions, displayed a fourfold increase in in vitro DNA-binding affinity and a 30.

Programmed RNA editing with an evolved bacterial adenosine deaminase.

Programmed RNA editing presents an attractive therapeutic strategy for genetic disease. In this study, we developed bacterial deaminase-enabled recoding of RNA (DECOR), which employs an evolved Escherichia coli transfer RNA adenosine deaminase, TadA8e, to deposit adenosine-to-inosine editing to CRISPR-specified sites in the human transcriptome. DECOR functions in a variety of cell types, including human lung fibroblasts, and delivers on-target activity similar to ADAR-overexpressing RNA-editing platforms with 88% lower off-target effects.

Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing.

RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites.

An adenine base editor variant expands context compatibility.

Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. Existing ABEs function most effectively when the target A is in a TA context. Here we evolve the Escherichia coli transfer RNA-specific adenosine deaminase (TadA) to generate TadA8r, which extends potent deoxyadenosine deamination to RA (R = A or G) and is faster in processing GA than TadA8.

An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity.

Compact CRISPR-Cas systems offer versatile treatment options for genetic disorders, but their application is often limited by modest gene-editing activity. Here we present enAsCas12f, an engineered RNA-guided DNA endonuclease up to 11.3-fold more potent than its parent protein, AsCas12f, and one-third of the size of SpCas9.

An outbreak of poisoning.

Background: The mushroom is reported to cause acute liver injury. It is found in Southern China, and has been previously associated with a high incidence of mortality.

Methods: We described a series of 10 patients with poisoning admitted to The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) in April 2022.

Transcriptome-wide profiling and quantification of N-methyladenosine by enzyme-assisted adenosine deamination.

N-methyladenosine (mA), the most abundant internal messenger RNA modification in higher eukaryotes, serves myriad roles in regulating cellular processes. Functional dissection of mA is, however, hampered in part by the lack of high-resolution and quantitative detection methods. Here we present evolved TadA-assisted N-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology that detects and quantifies mA by global adenosine deamination.

Experimental and Kinetic Studies of Ethylene Glycol Autoignition at High Temperatures.

As one of the simplest polyols with chemical properties of alcohol, ethylene glycol is considered as a renewable energy source and a model fuel for pyrolysis oil. In this work, autoignition characteristics of ethylene glycol have been investigated behind reflected shock waves. Experiments were conducted at pressures of 2, 5, and 10 atm, equivalence ratios of 0.

Structure-Activity Relationships of the Enterococcal Cytolysin.

Enterococcal cytolysin is a hemolytic virulence factor linked to human disease and increased patient mortality. Produced by pathogenic strains of , cytolysin is made up of two small, post-translationally modified peptides called CylL" and CylL". They exhibit a unique toxicity profile where lytic activity is observed for both mammalian cells and Gram-positive bacteria that is dependent on the presence of both peptides.

Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.

[This corrects the article DOI: 10.1039/D0SC01651A.].

Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.

Lanthipeptides are characterized by thioether crosslinks formed by post-translational modifications. The cyclization process that favors a single ring pattern over many other possible ring patterns has been the topic of much speculation. Recent studies suggest that for some systems the cyclization pattern and stereochemistry is determined not by the enzyme, but by the sequence of the precursor peptide.

CylA is a sequence-specific protease involved in toxin biosynthesis.

CylA is a subtilisin-like protein belonging to a recently expanded serine protease family related to class II lanthipeptide biosynthesis. As a leader peptidase, CylA is responsible for maturation of the enterococcal cytolysin, a lantibiotic important for Enterococcus faecalis virulence. In vitro reconstitution of CylA reveals that it accepts both linear and modified cytolysin peptides with a preference for cyclized peptides.

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity.

A key limitation of the use of the CRISPR-Cas9 system for genome editing and other applications is the requirement that a protospacer adjacent motif (PAM) be present at the target site. For the most commonly used Cas9 from Streptococcus pyogenes (SpCas9), the required PAM sequence is NGG. No natural or engineered Cas9 variants that have been shown to function efficiently in mammalian cells offer a PAM less restrictive than NGG.