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.     

PASTE: a high-throughput method for large DNA insertions

Prime editing (PE) enables precise genome editing at targeted locus without inducing double-stranded breaks (DSBs). Despite its precision, PE lacks the tendency to integrate large DNA fragments into the genome. Recently, Yarnall et al. reported clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 and an integrase-based system that conducts targeted integration of large DNA sequences (~36 kb) into the genome more efficiently.     

CONSTANS,a key-player connecting day length to seed size

Plants sense oscillation in the day length as a reliable seasonal cue to drive optimal vegetative and reproductive growth. A recent study by Yu et al. has revealed how day length regulates seed size through CONSTANS. The CONSTANS–APETALA2 module enables plants to optimize their reproductive growth based on their photoperiod response type.     

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.     

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.     

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.     

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.     

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.     

Newly evolved genes in the human lineage are functional

Genes restricted to a given species or lineage are mysterious. Many emerged de novo from ancestral noncoding genomic regions rather than from pre-existing genes. A new study by Vakirlis and colleagues shows that, in humans, many of these are associated with phenotypic effects, accelerating our understanding of their functional importance.     

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.     

Matching metabolic supply to demand optimizes microbial growth

Recent research has strengthened the notion that microbes allocate their biosynthetic capacity to maximize the growth rate, λ. Yet many microbes can grow substantially faster after laboratory evolution. Chure and Cremer advance a resource-allocation model, which they derive from first principles, that offers resolution to this conundrum.     

Plants can talk: a new era in plant acoustics

Plants release chemical signals to interact with their environment when exposed to stress. Khait and colleagues unveiled that plants ‘verbalize’ stress by emitting airborne sounds. These can train machine learning models to identify plant stressors. This unlocks a new path in plant-environment interactions research with multiple possibilities for future applications.     

Maternal plastid inheritance: two abating factors identified

Organelle DNAs (orgDNAs) in mitochondria and plastids are generally inherited from the maternal parent; however, it is unclear how their inheritance mode is controlled, particularly in the plastids of seed plants. Chung et al. identify two factors that affect maternal inheritance in tobacco plastids: cold temperature and DNA amount in pollen.     

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.     

Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models

RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevent analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to be present in the input. We present Arena (Atomic Reconstruction of RNA), which reconstructs a full atomic RNA structure from residues that can have as few as one atom. Arena first fills in missing atoms and then iteratively refines their placement to reduce nonideal geometries. We benchmarked Arena on a dataset of 361 RNA structures, where Arena achieves high accuracy and speed compared to other structure reconstruction programs. For example, Arena was used to reconstruct full atomic structures from a single phosphorus atom per nucleotide to, on average, within 3.63 Å RMSD of the experimental structure, while virtually removing all clashes and running in <3 s, which is 353× and 46× faster than state-of-the-art programs PDBFixer and C2A, respectively. The Arena source code is available at https://github.com/pylelab/Arena and the webserver at https://zhanggroup.org/Arena/.     

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.     

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.