Inferring secretory and metabolic pathway activity from omic data with secCellFie.

Understanding protein secretion has considerable importance in biotechnology and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience.

Inferring secretory and metabolic pathway activity from omic data with secCellFie.

Understanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience.

From observational to actionable: rethinking omics in biologics production.

As the era of omics continues to expand with increasing ubiquity and success in both academia and industry, omics-based experiments are becoming commonplace in industrial biotechnology, including efforts to develop novel solutions in bioprocess optimization and cell line development. Omic technologies provide particularly valuable 'observational' insights for discovery science, especially in academic research and industrial R&D; however, biomanufacturing requires a different paradigm to unlock 'actionable' insights from omics. Here, we argue the value of omic experiments in biotechnology can be maximized with deliberate selection of omic approaches and forethought about analysis techniques.

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data.

Understanding cellular metabolism is important across biotechnology and biomedical research and has critical implications in a broad range of normal and pathological conditions. Here, we introduce the user-friendly web-based platform ImmCellFie, which allows the comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. We explain how to set up a run using publicly available omics data and how to visualize the results.

Model-based assessment of mammalian cell metabolic functionalities using omics data.

Omics experiments are ubiquitous in biological studies, leading to a deluge of data. However, it is still challenging to connect changes in these data to changes in cell functions because of complex interdependencies between genes, proteins, and metabolites. Here, we present a framework allowing researchers to infer how metabolic functions change on the basis of omics data.

Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy.

Cancer immunotherapy has revolutionized treatment and led to an unprecedented wave of immuno-oncology research during the past two decades. In 2018, two pioneer immunotherapy innovators, Tasuku Honjo and James P. Allison, were awarded the Nobel Prize for their landmark cancer immunotherapy work regarding "cancer therapy by inhibition of negative immune regulation" -CTLA4 and PD-1 immune checkpoints.

From omics to Cellular mechanisms in mammalian cell factory development.

Mammalian cells have been used widely as biopharmaceutical cell factories due to their ability to make complex biotherapeutic proteins with human-compatible modifications. However, their application for some products has been hampered by low protein yields. Numerous studies have aimed to characterize cellular bottlenecks in the hope of boosting protein productivity, but the complexity of the underlying pathways and the diversity of the modifications have complicated cell engineering when relying solely on traditional methodologies.

The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection.

The recently discovered lytic polysaccharide monooxygenases (LPMOs), which cleave polysaccharides by oxidation, have been associated with bacterial virulence, but supporting functional data is scarce. Here we show that CbpD, the LPMO of Pseudomonas aeruginosa, is a chitin-oxidizing virulence factor that promotes survival of the bacterium in human blood. The catalytic activity of CbpD was promoted by azurin and pyocyanin, two redox-active virulence factors also secreted by P.

Systematically gap-filling the genome-scale metabolic model of CHO cells.

Objective: Chinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power.

Multiplex secretome engineering enhances recombinant protein production and purity.

Host cell proteins (HCPs) are process-related impurities generated during biotherapeutic protein production. HCPs can be problematic if they pose a significant metabolic demand, degrade product quality, or contaminate the final product. Here, we present an effort to create a "clean" Chinese hamster ovary (CHO) cell by disrupting multiple genes to eliminate HCPs.

Experiences of Young People with Harmful Sexual Behaviors in Services: A Qualitative Study.

Young people are responsible for a significant number of the sexual offenses that are committed every year. These young people are generally referred to specialist services for treatment. This article explores the health characteristics and service experiences of 117 young people with sexual behavior problems, and the issues that services face when working with them.

Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model.

Agrobacterium rhizogenes (or Rhizobium rhizogenes) is able to transform plant genomes and induce the production of hairy roots. We describe the use of A. rhizogenes in tomato (Solanum spp.

Exploring consensus in practice with youth who are sexually abusive: findings from a Delphi study of practitioner views in the United Kingdom and the Republic of Ireland.

This article presents the findings of a study exploring current levels of consensus among practitioners in the United Kingdom (UK) and the Republic of Ireland (ROI) about good practice in relation to youth who are sexually abusive. A three-stage Delphi procedure was used to survey the views of 78 practitioners, experienced in this field, on a range of matters relating to preferred responses to this population. The exercise indicated high levels of agreement that youth who are sexually abusive should be seen as a group clinically distinct from adult sex offenders and that all of their developmental needs, and their problematic behavior, should be targeted in intervention.