Variant-to-gene,gene-to-trait: finding new sleep genes through GWAS

Distilling insomnia genome-wide association study (GWAS) variants, Palermo and colleagues identified several genes that participate in sleep regulation in two different model organisms. This workflow sets off an innovative strategy to extract biological relevance from large human genomic databases.     

β2ARs: double edge sword in heart function

Deng and colleagues highlight the importance of understanding the divergent roles of β2-adrenoceptor (β₂AR) in high-fat diet-induced heart failure. β₂AR signaling has beneficial and detrimental effects depending on the context and level of activation. We discuss the importance of these findings and their implications in developing effective and safe therapies.     

Fine-tuning germline mutation rates across evolution

The germline mutation rate (GMR) sets the pace at which mutations, the raw material of evolution, are introduced into the genome. By sequencing a dataset of unprecedently broad phylogenetic scope, Bergeron et al. estimated species-specific GMR, offering numerous insights into how this parameter shapes and is shaped by life-history traits.     

pH regulates peptide–receptor perception

Diverse plant small peptides are perceived by their corresponding receptors to mediate local or long-distance intercellular communications in various developmental and adaptive programs; notably, the mechanisms of peptide–receptor perception remain largely unrevealed. Two reports (Liu et al.; Diaz-Ardila et al.) shed light on how pH regulates peptide–receptor perception.     

ParaSiteDB – A user-friendly database for managing a parasitological collection

ParaSiteDB is an application for arranging and managing a parasitological collection. It has been designed to provide a user-friendly, easily manageable and searchable site and is suitable for small to bigger collections.The source code of the application is available on GitHub: https://github.com/goobar4/aacrg.The demonstration version of the application is available on https://syrota.info/wormbasehttp://syrota.info/wormbase.     

Viral sponges sequester nucleotide signals to inactivate immunity

Bacteria synthesize specialized nucleotide signals to control anti-phage defense. Two papers – by Huiting et al. and Jenson et al. – now reveal that bacteriophages encode protein ‘sponges’ that sequester cyclic oligonucleotide immune signals and inactivate host antiviral immunity.     

Dual function of the CHS3-CSA1 immune receptor pair

Plant nucleotide-binding leucine-rich repeat (NLR) receptors mediate specific recognition of pathogen effectors to initiate effector-triggered immunity. Recently, studies by Schulze et al., Yang et al., and Gu et al. collectively show that the Arabidopsis (Arabidopsis thaliana) NLR pair CHS3-CSA1 acts through two distinct activation modes to recognize different pathogen effectors, thus revealing the dual function of the CHS3-CSA1 pair in plant disease resistance.     

Feeding the world sustainably: efficient nitrogen use

Globally, overuse of nitrogen (N) fertilizers in croplands is causing severe environmental pollution. In this context, Gu et al. suggest environmentally friendly and cost-effective N management practices and Hamani et al. highlight the use of microbial inoculants to improve crop yields, while reducing N-associated environmental pollution and N-fertilizer use.     

LigBind: Identifying Binding Residues for Over 1000 Ligands with Relation-Aware Graph Neural Networks

Identifying the interactions between proteins and ligands is significant for drug discovery and design. Considering the diverse binding patterns of ligands, the ligand-specific methods are trained per ligand to predict binding residues. However, most of the existing ligand-specific methods ignore shared binding preferences among various ligands and generally only cover a limited number of ligands with a sufficient number of known binding proteins. In this study, we propose a relation-aware framework LigBind with graph-level pre-training to enhance the ligand-specific binding residue predictions for 1159 ligands, which can effectively cover the ligands with a few known binding proteins. LigBind first pre-trains a graph neural network-based feature extractor for ligand-residue pairs and relation-aware classifiers for similar ligands. Then, LigBind is fine-tuned with ligand-specific binding data, where a domain adaptive neural network is designed to automatically leverage the diversity and similarity of various ligand-binding patterns for accurate binding residue prediction. We construct ligand-specific benchmark datasets of 1159 ligands and 16 unseen ligands, which are used to evaluate the effectiveness of LigBind. The results demonstrate the LigBind’s efficacy on large-scale ligand-specific benchmark datasets, and it generalizes well to unseen ligands. LigBind also enables accurate identification of the ligand-binding residues in the main protease, papain-like protease and the RNA-dependent RNA polymerase of SARS-CoV-2. The web server and source codes of LigBind are available at http://www.csbio.sjtu.edu.cn/bioinf/LigBind/ and https://github.com/YYingXia/LigBind/ for academic use.     

Naturally engineered plant microbiomes in resource-limited ecosystems

Nature-designed plant microbiomes may offer solutions to improve crop production and ecosystem restoration in less than optimum environments. Through a full exploration of metagenomic data, Camargo et al. showed that a previously unknown microbial diversity enhances nutrient mobilization in stress-adapted plants.     

Protein circuit design using de novo proteins

Protein-based biological circuits enable customized control of cellular functions, and de novo protein design enables circuit functionalities that are not possible by repurposing natural proteins. Here, I highlight recent progress in protein circuit design, including CHOMP, developed by Gao et al., and SPOC, developed by Fink et al.     

Multi-omic genetic scores advance disease research

Multi-omic analysis is an effective approach for dissecting the mechanisms of diseases; however, collecting multi-omic data in large populations is time-consuming and costly. Recently, Xu et al. developed genetic scores for multi-omic traits and demonstrated their utilization to gain novel insights, advancing the application of multi-omic data in disease research.     

CryoEM shows the active dynein complex on microtubules

In a recent study, Chaaban and Carter use cryo-electron microscopy (cryo-EM) and an innovative data-processing pipeline to determine the first high-resolution structure of the dynein–dynactin–BICDR1 complex assembled on microtubules. The structure of the complex reveals novel stoichiometry and provides new mechanistic insight into dynein function and mechanism.     

Measuring tree-ring widths using the CooRecorder software application

We present a brief overview of how to measure tree-ring widths in the software application CooRecorder (Cybis Elektronik & Data AB) for tree-ring analysis complementing two video tutorials. The first tutorial covers the basics of opening files, measuring ring widths, preliminary crossdating with a reference chronology, and setting dates. The second tutorial covers setting earlywood-latewood boundaries, measuring across cracks, inserting locally absent or missing rings, manual adjustments, and metadata. The video tutorials can be found here https://www.youtube.com/watch?v=c-GNKHVUj9I and here https://www.youtube.com/watch?v=xO7Phc93xyM&t=3s. Videos have been closed-captioned in English. Video is also accessible via Mendeley Data, https://doi.org/10.17632/r3v7236kkz.1.     

A comprehensive review on the phytochemistry,pharmacokinetics, and antidiabetic effect of Ginseng

BackgroundRadix Ginseng, one of the well-known medicinal herbs, has been used in the management of diabetes and its complications for more than 1000 years.PurposeThe aim of this review is devoted to summarize the phytochemistry and pharmacokinetics of Ginseng, and provide evidence for the antidiabetic effects of Ginseng and its ingredients as well as the underlying mechanisms involved.MethodsFor the purpose of this review, the following databases were consulted: the PubMed Database (https://pubmed.ncbi.nlm.nih.gov), Chinese National Knowledge Infrastructure (http://www.cnki.net), National Science and Technology Library (http://www.nstl.gov.cn/), Wanfang Data (http://www.wanfangdata.com.cn/) and the Web of Science Database (http://apps.webofknowledge.com/).ResultsGinseng exhibits glucose-lowering effects in different diabetic animal models. In addition, Ginseng may prevent the development of diabetic complications, including liver, pancreas, adipose tissue, skeletal muscle, nephropathy, cardiomyopathy, retinopathy, atherosclerosis and others. The main ingredients of Ginseng include ginsenosides and polysaccharides. The underlying mechanisms whereby this herb exerts antidiabetic activities may be attributed to the regulation of multiple signaling pathways, including IRS1/PI3K/AKT, LKB1/AMPK/FoxO1, AGEs/RAGE, MAPK/ERK, NF-κB, PPARδ/STAT3, cAMP/PKA/CERB and HIF-1α/VEGF, etc. The pharmacokinetic profiles of ginsenosides provide valuable information on therapeutic efficacy of Ginseng in diabetes. Although Ginseng is well-tolerated, dietary consumption of this herb should follow the doctors’ advice.ConclusionGinseng may offer an alternative strategy in protection against diabetes and its complications through the regulations of the multi-targets via various signaling pathways. Efforts to understand the underlying mechanisms with strictly-controlled animal models, combined with well-designed clinical trials and pharmacokinetic evaluation, will be important subjects of the further investigations and weigh in translational value of this herb in diabetes management.     

Chemical constituents from Valeriana jatamansi

Phytochemical study of Valeriana jatamansi Jones afforded 45 compounds, including twenty-three iridoids (1–23), five sesquiterpenes (24–28), three steroids (29–31) and fourteen lignins (32–45). The structures of these compounds were assigned by detailed interpretation of spectroscopic data (1D and 2D NMR, HRESIMS) and comparisons with the published data. This is the first report of isolation of compounds (1–6, 10, 21, 25, 41, 43, 44, 45) from Valerianaceae, compounds (13, 27, 39) within the genus Valeriana and compound 30 from V. jatamans. The chemotaxonomic data can support the genus Valeriana being accepted as a member of transitional taxa between the family Valerianaceae and Caprifoliaceae.     

Unleashing the potential of peptides in agriculture and beyond

Peptides display a broad range of regulatory functions. Ormancey et al. recently identified an important new mechanism – complementary peptides (cPEPs) – that provide a versatile means to control cell functions. We draw a parallel between RNA and peptide biology, and discuss new routes of investigation and industrial applications opened by this work.