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.     

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.     

Q-NET – a new scholarly network on quantitative wood anatomy

Quantitative wood anatomy (QWA) is a dynamic research approach of increasing interest that can provide answers to a wide range of research questions across different disciplines. However, the lack of common protocols and knowledge gaps hinder the realisation of the full potential of QWA. Therefore, we established the new community-based network Q-NET to provide an open interdisciplinary platform for exchange and research around QWA. Q-NET (https://qwa-net.com) combines an online knowledge and exchange base with virtual workshops. The first two workshops each attracted more than 125 participants from around the world, demonstrating the community's interest in QWA and this virtual way of networking and collaborating. Indeed, virtual networks such as Q-NET could increase the inclusiveness, efficiency and sustainability of scientific collaboration while providing additional training and teaching opportunities for early career scientists, both of which complement in-person conferences and workshops.     

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.     

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/.     

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.     

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.     

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.     

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.     

A novel nest‐monitoring camera system using a Raspberry Pi micro‐computer

The utility, availability, cost‐effectiveness, and reliability of prefabricated video systems designed to monitor wildlife have lagged behind the unique and varied needs of many researchers. Many systems are limited by inflexible video settings, lack of adequate data storage, and cannot be programmed by the user. More sophisticated systems can be cost prohibitive, and the literature describing remote wildlife video monitoring has, for the most part, not incorporated advances in camera and computer technology. Here, we present details of a pilot study to design and construct a lower cost (US $340) nest camera system to record the behavior of Acorn Woodpeckers (Melanerpes formicivorus) in artificial tree cavity nests. This system incorporates a Raspberry Pi micro‐computer, Pi NoIR infrared camera, a wireless adapter to transmit video over the Internet, and Deka rechargeable gel batteries for power. We programmed the system to motion‐sense, to record exclusively during daylight hours, and to automatically upload videos to the cloud over wireless Internet. The Raspberry Pi micro‐computer does not require advanced programming or electrical engineering skills to build and configure and, because it is programmable, provides unprecedented flexibility for field researchers who wish to configure the system to the specific needs of their study.     

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.     

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.     

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.     

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.     

Staying vigilant: NLR monitors virus invasion

Phytohormones play important roles in plant immunity. Recently, Chen et al. discovered that the tomato spotted wilt virus attacks the plant hormone receptor to promote infection. Plants evolved an immune receptor to mimic the attacked hormone receptors to recognize the virus, thereby activating a robust immune response.     

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.     

An miRNA with a major impact on stress

miRNAs regulate mRNAs, including those important for synapse function in the brain. Mucha and colleagues recently identified a novel miRNA–mRNA interaction in the basolateral amygdala that acts as a homeostatic counter to stress-induced anxiety and synaptic changes, suggesting miRNAs as potential avenues for therapeutic intervention in anxiety disorders.     

Sense the moist and feel the heat: mosquito host and oviposition site detection

Laursen et al. identified coreceptor Ir93a that is required for humidity and thermal sensing in the mosquito species Anopheles gambiae and Aedes aegypti. Behavioural studies with mutant mosquitoes with disrupted Ir93a revealed that they were less attracted to a blood meal source and oviposition site at close distance.