Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.

Re-epithelialization of whole porcine kidneys with renal epithelial cells.

Decellularized porcine kidneys were recellularized with renal epithelial cells by three methods: perfusion through the vasculature under high pressure, perfusion through the ureter under high pressure, or perfusion through the ureter under moderate vacuum. Histology, scanning electron microscopy, confocal microscopy, and magnetic resonance imaging were used to assess vasculature preservation and the distribution of cells throughout the kidneys. Cells were detected in the magnetic resonance imaging by labeling them with iron oxide. Perfusion of cells through the ureter under moderate vacuum (40 mmHg) produced the most uniform distribution of cells throughout the kidneys.

The impact of decellularization agents on renal tissue extracellular matrix.

The combination of patient-specific cells with scaffolds obtained from natural sources may result in improved regeneration of human tissues. Decellularization of the native tissue is the first step in this technology. Effective decellularization uses agents that lyse cells and remove all cellular materials, leaving intact collagenous extracellular matrices (ECMs). Removing cellular remnants prevents an immune response while preserving the underlying structure. In this study, the impact of five decellularization agents (0.1 N NaOH, 1% peracetic acid, 3% Triton X-100, 1% sodium dodecyl sulfate (SDS), and 0.05% trypsin/EDTA) on renal tissue was examined using slices of porcine kidneys. The NaOH solution induced the most efficient cell removal, and resulted in the highest amount of cell viability and proliferation after recellularization, although it also produced the most significant damage to collagenous fiber networks, glycosaminoglycans (GAGs) and fibroblast growth factor (FGF). The SDS solution led to less severe damage to the ECM structure but it resulted in lower metabolic activity and less proliferation. Peracetic acid and Triton X-100 resulted in minimum disruption of ECMs and the most preserved GAGs and FGF. However, these last two agents were not as efficient in removing cellular materials as NaOH and SDS, especially peracetic acid, which left more than 80% of cellular material within the ECM. As a proof of principle, after completing the comparison studies using slices of renal ECM, the NaOH process was used to decellularize a whole kidney, with good results. The overall results demonstrate the significant effect of cell lysing agents and the importance of developing an optimized protocol to avoid extensive damage to the ECM while retaining the ability to support cell growth.

Current Cell-Based Strategies for Whole Kidney Regeneration.

Chronic kidney diseases affect thousands of people worldwide. Although hemodialysis alleviates the situation by filtering the patient's blood, it does not replace other kidney functions such as hormone release or homeostasis regulation. Consequently, orthotopic transplantation of donor organs is the ultimate treatment for patients suffering from end-stage renal failure. Unfortunately, the number of patients on the waiting list far exceeds the number of donors. In addition, recipients must remain on immunosuppressive medications for the remainder of their lives, which increases the risk of morbidity due to their weakened immune system. Despite recent advancements in whole organ transplantation, 40% of recipients will face rejection of implanted organs with a life expectancy of only 10 years. Bioengineered patient-specific kidneys could be an inexhaustible source of healthy kidneys without the risk of immune rejection. The purpose of this article is to review the pros and cons of several bioengineering strategies used in recent years and their unresolved issues. These strategies include repopulation of natural scaffolds with a patient's cells, de-novo generation of kidneys using patient-induced pluripotent stem cells combined with stepwise differentiation, and the creation of a patient's kidney in the embryos of other mammalian species.