HUH Endonuclease: A Sequence-specific Fusion Protein Tag for Precise DNA-Protein Conjugation.

Synthetic DNA-protein conjugates have found widespread applications in diagnostics and therapeutics, prompting a growing interest in developing chemical biology methodologies for the precise and site-specific preparation of covalent DNA-protein conjugates. In this review article, we concentrate on techniques to achieve precise control over the structural and site-specific aspects of DNA-protein conjugates. We summarize conventional methods involving unnatural amino acids and self-labeling proteins, accompanied by a discussion of their potential limitations.

Stratification of dissolved organic matter in the upper 5000 m water column in the western Pacific Ocean.

Marine dissolved organic matter (DOM) is a principal reservoir involved in biogeochemical cycles and exerts a pivotal influence on global carbon flux dynamics. In this study, excitation-emission matrix fluorescence spectroscopy combined with parallel factor analysis (EEM-PARAFAC) was conducted on 230 DOM samples collected from 21 sites between February and April 2022 in the Western Pacific Ocean (WPO). We identified five distinct fluorescence peaks (peaks B, T, A, C, and M), predominantly protein-like and humic-like components.

Responses of biological traits of macrobenthic fauna to a eutrophication gradient in a semi-enclosed bay, China.

The impacts of eutrophication on benthic ecological functions are of increasing concern in recent years. In order to assess the response of macrobenthic fauna to increasing eutrophication, two field sampling surveys were conducted during the summer (July-August 2020) and autumn (October-November 2020) from offshore, nearshore to estuarine sediments in Bohai Bay, northern China. Biological trait analysis was employed for the assessment of macrofaunal samples.

A snapshot on vertical variability of dissolved organic matter in the epilagic zone of the eastern Indian Ocean.

Marine dissolved organic matter (DOM) plays an important role in aquatic ecosystems and is an essential reservoir of organic carbon in the marine carbon cycle. In this study, seawater DOM samples from 33 stations were collected in spring 2022 (April to May, 20 stations) and autumn 2020 (October to November, 13 stations) to better characterize and compare DOM variability within 200 m water layer in the eastern Indian Ocean (EIO). Hydrological parameters, nutrients and spectroscopic indices were calculated and evaluated for two cruises.

Applying causal discovery to single-cell analyses using CausalCell.

Correlation between objects is prone to occur coincidentally, and exploring correlation or association in most situations does not answer scientific questions rich in causality. Causal discovery (also called causal inference) infers causal interactions between objects from observational data. Reported causal discovery methods and single-cell datasets make applying causal discovery to single cells a promising direction.

Variations in dissolved organic matter chemistry on a vertical scale in the eastern Indian Ocean.

Oceans cover approximately 71% of the Earth's surface area, which is why some people refer to the Earth as a large water sphere. Marine dissolved organic matter (DOM) constitutes the main carbon pool for biogeochemical cycles and plays an important role in global carbon dynamics. Here, the molecular composition and component characteristics of surface (5 m), deep chlorophyll maximum (DCM), and deep (2000 m) layer DOM in the eastern Indian Ocean (EIO) were investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and three-dimensional fluorescence spectroscopy.

enables fast and accurate genome-wide lncRNA/DNA binding prediction.

Many long noncoding RNAs (lncRNAs) can bind to DNA sequences proximal and distal to abundant genes, thereby regulating gene expression by recruiting epigenomic modification enzymes to binding sites. Because a lncRNA's target genes scattering in a genome have correlated functions, epigenetic analyses should often be genome-wide on both genome and transcriptome levels. Multiple tools have been developed for predicting lncRNA/DNA binding, but fast and accurate genome-wide prediction remains a challenge.

Pipelines for cross-species and genome-wide prediction of long noncoding RNA binding.

Abundant long, noncoding RNAs (lncRNAs) in mammals can bind to DNA sequences and recruit histone- and DNA-modifying enzymes to binding sites to epigenetically regulate target genes. However, most lncRNAs' binding motifs and target sites are unknown. The large numbers of lncRNAs and target sites in the whole genome make it infeasible to examine lncRNA binding to DNA purely experimentally.