Cellular Processes

Although cells in the nervous system contain all the cellular machinery that exists in other cells throughout the body, nervous system cells have many specialized functions that present unique challenges in the maintenance of cellular functionality and homeostasis. The unique morphology of neurons demands elaborate cytoarchitecture, energy production, and cellular processing machinery that are unparalleled in other parts of the body. This chapter presents a broad overview of cellular processes related to the cytoskeleton, axonal transport, protein processing, and energy metabolism within the nervous system. Breakdowns of these intricate processes are involved in many diseases of the nervous system, which are discussed in subsequent chapters.

High-throughput single-cell TCR - pMHC dissociation rate measurements performed by an autonomous microfluidic cellular processing unit

We developed an integrated microfluidic cellular processing unit (mCPU) capable of autonomously isolating single cells, perform, measure, and on-the-fly analyze cell-surface dissociation rates, followed by recovery of selected cells. We performed proof-of-concept, high- throughput single-cell experiments characterizing pMHC-TCR interactions on live CD8 T cells. The mCPU platform analyzed TCR-pMHC dissociation rates with a throughput of 50 cells per hour and hundreds of cells per run, and we demonstrate that cells can be selected, enriched, and easily recovered from the device.

Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast

Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains.

Medically Important Alterations in Transport Function and Trafficking of ABCG2

Several polymorphisms and mutations in the human ABCG2 multidrug transporter result in reduced plasma membrane expression and/or diminished transport function. Since ABCG2 plays a pivotal role in uric acid clearance, its malfunction may lead to hyperuricemia and gout. On the other hand, ABCG2 residing in various barrier tissues is involved in the innate defense mechanisms of the body; thus, genetic alterations in ABCG2 may modify the absorption, distribution, excretion of potentially toxic endo- and exogenous substances. In turn, this can lead either to altered therapy responses or to drug-related toxic reactions. This paper reviews the various types of mutations and polymorphisms in ABCG2, as well as the ways how altered cellular processing, trafficking, and transport activity of the protein can contribute to phenotypic manifestations. In addition, the various methods used for the identification of the impairments in ABCG2 variants and the different approaches to correct these defects are overviewed.

The kidney produces a non-polymerizing form of Uromodulin that associates with reduced risk of acute kidney injury

Uromodulin (Tamm-Horsfall protein, THP) is a glycoprotein uniquely produced in the kidney. It is released by cells of the thick ascending limbs (TAL) apically in the urine, and basolaterally in the renal interstitium and systemic circulation. Processing of mature urinary THP, which polymerizes into supra-molecular filaments, requires cleavage of an external hydrophobic patch (EHP) at the C terminus. However, THP in the circulation is not polymerized, and it remains unclear if non-aggregated forms of THP exist natively in the urine. We propose that an alternative processing path, which retains the EHP domain, can lead to a non-polymerizing form of THP. We have generated an antibody that specifically recognizes THP with retained EHP (THP+EHP) and established its presence in the urine in a non-polymerized native state. In the human kidney, THP+EHP predominantly co-localized with urinary THP in TAL cells, but it was also detected, at lower levels, in other tubular segments. We then developed a customized ELISA to measure THP+EHP and used it on urine and plasma samples from a small cohort of patients hospitalized with liver cirrhosis. On admission, urinary THP+EHP, but not total THP, was significantly lower in patients who subsequently developed acute kidney injury during hospitalization. THP+EHP was also detected in the plasma, albeit at very low concentrations. Our findings uncover novel insights into uromodulin biology by establishing the presence of an alternative path for cellular processing. Our proof-of-principle findings in patients warrant further investigations to establish the utility of THP+EHP as a sensitive biomarker of kidney health and susceptibility to injury.

Effect of surface energy and roughness on cell adhesion and growth – facile surface modification for enhanced cell culture

In vitro, cellular processing on polymeric surfaces is fundamental to the development of biosensors, scaffolds for tissue engineering and transplantation.

GRASP and Iterated Local Search-Based Cellular Processing algorithm for Precedence-Constraint Task List Scheduling on Heterogeneous Systems

High-Performance Computing systems rely on the software’s capability to be highly parallelized in individual computing tasks. However, even with a high parallelization level, poor scheduling can lead to long runtimes; this scheduling is in itself an NP-hard problem. Therefore, it is our interest to use a heuristic approach, particularly Cellular Processing Algorithms (CPA), which is a novel metaheuristic framework for optimization. This framework has its foundation in exploring the search space by multiple Processing Cells that communicate to exploit the search and in the individual stagnation detection mechanism in the Processing Cells. In this paper, we proposed using a Greedy Randomized Adaptive Search Procedure (GRASP) to look for promising task execution orders; later, a CPA formed with Iterated Local Search (ILS) Processing Cells is used for the optimization. We assess our approach with a high-performance ILS state-of-the-art approach. Experimental results show that the CPA outperforms the previous ILS in real applications and synthetic instances.

Similarities and Differences in Cellular Processing of Biologically Relevant Nanoparticles

Nanoparticles are endocytosed and trafficked within cells by selecting one or more of the cell's intrinsic processing pathways. However, general rules which drive this selection have not yet been defined. Therefore, each nanoparticle has to be investigated separately to determine its endocytosis and intracellular trafficking pathways. By using cryo SXT to investigate the cellular interaction of two different nanoparticles, we have uncovered some general rules about nanoparticle interactions with cells. Our results highlight not only the importance of cryo-SXT for nanoparticle investigation in the medical field, but also demonstrate that a well-controlled analysis makes it possible to discern general rules about cell-nanoparticle interactions.

Challenges in optimizing RNA nanostructures for large-scale production and controlled therapeutic properties

Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.