Cell wall polysaccharides from macauba pulp (Acrocomia aculeata L.): Fractionation and characterization of their chemical and rheological properties.

Macauba fruit pulp (Acrocomia aculeata) is an emerging oil source. After de-oiling, the macauba pulp meal (MPM) offers a dietary fiber content of 40-50 %, which mainly comprises cell wall polysaccharides (CWP). The present work aimed to assess the potential of MPM as an innovative source of sustainable food polysaccharides.

Predicting cell morphological responses to perturbations using generative modeling.

Advancements in high-throughput screenings enable the exploration of rich phenotypic readouts through high-content microscopy, expediting the development of phenotype-based drug discovery. However, analyzing large and complex high-content imaging screenings remains challenging due to incomplete sampling of perturbations and the presence of technical variations between experiments. To tackle these shortcomings, we present IMage Perturbation Autoencoder (IMPA), a generative style-transfer model predicting morphological changes of perturbations across genetic and chemical interventions.

Precursors of exhausted T cells are preemptively formed in acute infection.

T cell exhaustion limits effector T cell function in chronic infection and tumors. The development of these hypofunctional T cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T cell populations in the early phase of acute infections.

Contribution of mozambioside roasting products to coffee's bitter taste.

Roasting degrades the coffee compound mozambioside (1) into several products, including 17-O-β-D-glucosyl-11-hydroxycafestol-2-one (2), 11-O-β-D-glucosyl-16-desoxycafestol-2-one (3), 11-O-β-D-glucosyl-(S)-16-desoxy-17-oxocafestol-2-one (4), 11-O-β-D-glucosyl-15,16-dehydrocafestol-2-one (5), 11-O-β-D-glucosyl-(R)-16-desoxy-17-oxocafestol-2-one (6), bengalensol (7), and 11-hydroxycafestol-2-one (8). A UHPLC-MS/MS method was established to quantify 1-8 and monitor their formation during authentic coffee roasting. Concentrations of 1 and the dominant roasting products 4, 5, and 7 ranged from 21.

Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer's Disease.

The complex roles of myeloid cells, including microglia and perivascular macrophages, are central to the neurobiology of Alzheimer's disease (AD), yet they remain incompletely understood. Here, we profiled 832,505 human myeloid cells from the prefrontal cortex of 1,607 unique donors covering the human lifespan and varying degrees of AD neuropathology. We delineated 13 transcriptionally distinct myeloid subtypes organized into 6 subclasses and identified AD-associated adaptive changes in myeloid cells over aging and disease progression.

Considerations for building and using integrated single-cell atlases.

The rapid adoption of single-cell technologies has created an opportunity to build single-cell 'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear.

Bilingual language model for protein sequence and structure.

Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences.

Understanding the role of in atopic dermatitis: strain diversity, microevolution, and prophage influences.

Atopic dermatitis (AD) is a prevalent inflammatory skin disorder characterized by chronic inflammation, skin barrier dysfunction, and microbial dysbiosis, with playing a significant role in its pathogenesis. This paper explores the strain diversity and microevolution of within AD patients, emphasizing how specific strains adapt to the altered skin environment, exacerbating the condition. The review emphasizes the significance of variation in specific functional genes among strains, which enhances their ability to adapt to different microenvironments and shapes their pathogenic potential.

Expert-guided protein language models enable accurate and blazingly fast fitness prediction.

Motivation: Exhaustive experimental annotation of the effect of all known protein variants remains daunting and expensive, stressing the need for scalable effect predictions. We introduce VespaG, a blazingly fast missense amino acid variant effect predictor, leveraging protein language model (pLM) embeddings as input to a minimal deep learning model.

Results: To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from the human proteome applying the multiple sequence alignment-based effect predictor GEMME as a pseudo standard-of-truth.

An integrated transcriptomic cell atlas of human neural organoids.

Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to study human brain development, evolution and disease. However, it is unclear which parts of the human brain are covered by existing protocols, and it has been difficult to quantitatively assess organoid variation and fidelity. Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.

Probe set selection for targeted spatial transcriptomics.

Targeted spatial transcriptomic methods capture the topology of cell types and states in tissues at single-cell and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is crucial for capturing the spatial signals present in a tissue. This requires selecting the most informative, yet minimal, set of genes to profile (gene set selection) for which it is possible to build probes (probe design).

Structural variation in the pangenome of wild and domesticated barley.

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes.

Nonvesicular lipid transfer drives myelin growth in the central nervous system.

Oligodendrocytes extend numerous cellular processes that wrap multiple times around axons to generate lipid-rich myelin sheaths. Myelin biogenesis requires an enormously productive biosynthetic machinery for generating and delivering these large amounts of newly synthesized lipids. Yet, a complete understanding of this process remains elusive.

Fava Bean Protein Nanofibrils Modulate Cell Membrane Interfaces for Biomolecular Interactions as Unveiled by Atomic Force Microscopy.

Functional amyloids (protein nanofibrils, PNF) synthesized from plant sources exhibit unique physicochemical and nanomechanical properties that could improve food texture. While environmental factors affecting PNFs are well-known, scientific evidence on how cells (focus on the oral cavity) respond to them under physiological conditions is lacking. Self-assembled PNFs synthesized from fava bean whole protein isolate show a strong pH- and solvent-dependent morphology and elasticity modification measured by atomic force microscopy (AFM).

Oxygen Consumption in Filamentous Pellets of Aspergillus niger: Microelectrode Measurements and Modeling.

Filamentous fungi cultivated as biopellets are well established in biotechnology industries. A distinctive feature of filamentous fungi is that hyphal growth and fungal morphology affect product titers and require tailored process conditions. Within the pellet, mass transfer, substrate consumption, and biomass formation are intricately linked to the local hyphal fraction and pellet size.

Mapping lineage-traced cells across time points with moslin.

Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making. Recent computational approaches combine both modalities into cellular trajectories; however, they cannot make use of all available lineage information in destructive time-series experiments. Here, we present moslin, a Gromov-Wasserstein-based model to couple cellular profiles across time points based on lineage and gene expression information.

Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport.

The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases.

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells.