Evidence-based unification of potato gene models with the UniTato collaborative genome browser.

Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant re-analysis, and leads to missing or wrongly annotated genes. Here, we unify the recent potato double monoploid v4 and v6 gene models by developing an automated merging protocol, resulting in a Unified poTato genome model (UniTato). We subsequently established an Apollo genome browser (unitato.nib.si) that enables public access to UniTato and further community-based curation. We demonstrate how the UniTato resource can help resolve problems with missing or misplaced genes and can be used to update or consolidate a wider set of gene models or genome information. The automated protocol, genome annotation files, and a comprehensive translation table are provided at github.com/NIB-SI/unitato.

CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues.

Motivation: Cell-type deconvolution methods aim to infer cell composition from bulk transcriptomic data. The proliferation of developed methods coupled with inconsistent results obtained in many cases, highlights the pressing need for guidance in the selection of appropriate methods. Additionally, the growing accessibility of single-cell RNA sequencing datasets, often accompanied by bulk expression from related samples enable the benchmark of existing methods. Results: In this study, we conduct a comprehensive assessment of 31 methods, utilizing single-cell RNA-sequencing data from diverse human and mouse tissues. Employing various simulation scenarios, we reveal the efficacy of regression-based deconvolution methods, highlighting their sensitivity to reference choices. We investigate the impact of bulk-reference differences, incorporating variables such as sample, study and technology. We provide validation using a gold standard dataset from mononuclear cells and suggest a consensus prediction of proportions when ground truth is not available. We validated the consensus method on data from the stomach and studied its spillover effect. Importantly, we propose the use of the critical assessment of transcriptomic deconvolution (CATD) pipeline which encompasses functionalities for generating references and pseudo-bulks and running implemented deconvolution methods. CATD streamlines simultaneous deconvolution of numerous bulk samples, providing a practical solution for speeding up the evaluation of newly developed methods. Availability and implementation: https://github.com/Papatheodorou-Group/CATD_snakemake.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.

Wood-Veneer-Reinforced Mycelium Composites for Sustainable Building Components.

The demand for building materials has been constantly increasing, which leads to excessive energy consumption for their provision. The looming environmental consequences have triggered the search for sustainable alternatives. Mycelium, as a rapidly renewable, low-carbon natural material that can withstand compressive forces and has inherent acoustic and fire-resistance properties, could be a potential solution to this problem. However, due to its low tensile, flexural and shear strength, mycelium is not currently widely used commercially in the construction industry. Therefore, this research focuses on improving the structural performance of mycelium composites for interior use through custom robotic additive manufacturing processes that integrate continuous wood fibers into the mycelial matrix as reinforcement. This creates a novel, 100% bio-based, wood-veneer-reinforced mycelium composite. As base materials, Ganoderma lucidum and hemp hurds for mycelium growth and maple veneer for reinforcement were pre-selected for this study. Compression, pull-out, and three-point bending tests comparing the unreinforced samples to the veneer-reinforced samples were performed, revealing improvements on the bending resistance of the reinforced samples. Additionally, the tensile strength of the reinforcement joints was examined and proved to be stronger than the material itself. The paper presents preliminary experiment results showing the effect of veneer reinforcements on increasing bending resistance, discusses the potential benefits of combining wood veneer and mycelium's distinct material properties, and highlights methods for the design and production of architectural components.

CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences.

RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.