Macromolecular crowding effects on transcription and translation are regulated by free magnesium ion

Bioengineering lipid-based synthetic cells for therapeutic protein delivery

Synthetic cells (SCs) offer a promising approach for therapeutic protein delivery, combining principles from synthetic biology and drug delivery. Engineered to mimic natural cells, SCs provide biocompatibility and versatility, with precise control over their architecture and composition. Protein production is essential in living cells, and SCs aim to replicate this process using compartmentalized cell-free protein synthesis systems within lipid bilayers. Lipid bilayers serve as favored membranes in SC design due to their similarity to the biological cell membrane. Moreover, engineering lipidic membranes enable tissue-specific targeting and immune evasion, while stimulus-responsive SCs allow for triggered protein production and release. This Review explores lipid-based SCs as platforms for therapeutic protein delivery, discussing their design principles, functional attributes, and translational challenges and potential.

A Clostridioides difficile cell-free gene expression system for prototyping and gene expression analysis

Clostridioides difficile is an obligate anaerobic, Gram-positive bacterium that produces toxins. Despite technological progress, conducting gene expression analysis of C. difficile under different conditions continues to be labor-intensive. Therefore, there is a demand for simplified tools to investigate the transcriptional and translational regulation of C. difficile. The cell-free gene expression (CFE) system has demonstrated utility in various applications, including prototyping, protein production, and in vitro screening. In this study, we developed a C. difficile CFE system capable of in vitro transcription and translation (TX-TL) in the presence of oxygen. Through optimization of cell extract preparation and reaction systems, we increased the protein yield significantly. Furthermore, our observations indicated that this system exhibited higher protein yield using linear DNA templates than circular plasmids for in vitro expression. The prototyping capability of the C. difficile CFE system was assessed using a series of synthetic Clostridium promoters, demonstrating a good correlation between in vivo and in vitro expression. Additionally, we tested the expression of tcdB and tcdR from clinically relevant C. difficile strains using the CFE system, confirming higher toxin expression of the hypervirulent strain R20291. We believe that the CFE system can not only serve as a platform for in vitro protein synthesis and genetic part prototyping but also has the potential to be a simplified model for studying metabolic regulations in Clostridioides difficile.IMPORTANCEClostridioides difficile has been listed as an urgent threat due to its antibiotic resistance, and it is crucial to conduct gene expression analysis to understand gene functionality. However, this task can be challenging, given the need to maintain the bacterium in an anaerobic environment and the inefficiency of introducing genetic material into C. difficile cells. Conversely, the C. difficile cell-free gene expression (CFE) system enables in vitro transcription and translation in the presence of oxygen within just half an hour. Furthermore, the composition of the CFE system is adaptable, permitting the addition or removal of elements, regulatory proteins for example, during the reaction. As a result, this system could potentially offer an efficient and accessible approach to accelerate the study of gene expression and function in Clostridioides difficile.

Macromolecular crowding: Sensing without a sensor

All living cells are crowded with macromolecules. Crowding can directly modulate biochemical reactions to various degrees depending on the sizes, shapes, and binding affinities of the reactants. Here, we explore the possibility that cells can sense and adapt to changes in crowding through the widespread modulation of biochemical reactions without the need for a dedicated sensor. Additionally, we explore phase separation as a general physicochemical response to changes in crowding, and a mechanism to both transduce information and physically restore crowding homeostasis.

A Comprehensive Comparison of Rapid RNA Extraction Methods for Detection of SARS-CoV-2 as the Infectious Agent of the Upper Respiratory Tract using Direct RT-LAMP Assay

Background

The current COVID-19 pandemic has highlighted the need for faster and more cost-effective diagnostic methods. The RNA extraction step in current diagnostic methods, such as real-time qPCR, increases the cost and time required for testing. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a promising technique for developing diagnostic tests with desired sensitivity and specificity without the need for RNA extraction.

Materials and Methods

An RT-LAMP assay was developed to detect SARS-CoV-2 with a sensitivity of 0.5 copies of positive control plasmid per microliter in 40 min. Several rapid RNA extraction protocols were evaluated using different reagents, including bovine serum albumin, Triton X-100, Tween 20, proteinase K, guanidine hydrochloride, guanidinium isothiocyanate (GITC), and thermal treatment. Finally, the sensitivity and specificity of the developed direct RT-LAMP were determined using 150 upper respiratory tract samples.

Results

Method 10 was selected as the most efficient protocol for the RNA extraction step. The sensitivity and specificity of the developed direct RT-LAMP assay with clinical samples were estimated at 98.4% and 88.8%, respectively.

Conclusion

These results suggest that the combination of GITC and Triton X-100 detergent is a highly efficient method for RNA extraction and direct RT-LAMP detection of SARS-CoV-2 in clinical samples, providing a valuable tool for the rapid and cost-effective diagnosis of COVID-19.

Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits

Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.

Neuroprotective effect of magnesium supplementation on cerebral ischemic diseases

Ischemic encephalopathy is associated with a high mortality and rate of disability. The most common type of ischemic encephalopathy, ischemic stroke, is the second leading cause of death in the world. At present, the main treatment for ischemic stroke is to reopen blocked blood vessels. However, despite revascularization, many patients are not able to achieve good functional results. At the same time, the strict time window (<4.5 h) of thrombolytic therapy limits clinical application. Therefore, it is important to explore effective neuroprotective drugs for the treatment of ischemic stroke. Magnesium is a natural calcium antagonist, which exerts neuroprotective effects through various mechanisms. However, while most basic studies have shown that magnesium supplementation can help treat cerebral ischemia, intravenous magnesium supplementation in large clinical trials has failed to improve prognosis of ischemic patients. Therefore, we review the basic and clinical studies of magnesium supplementation for cerebral ischemia. According to the route of administration, treatment can be divided into intraperitoneal magnesium supplementation, intravenous magnesium supplementation, arterial magnesium supplementation and intracranial magnesium supplementation. We also summarized the potential influencing factors of magnesium ion intervention in cerebral ischemia injury. Finally, in combination with influencing factors derived from basic research, this article proposes three future research directions, including magnesium supplementation into the circulatory system combined with magnesium supplementation in the lateral ventricle, magnesium supplementation in the lateral ventricle combined with hypothermia therapy, and lateral ventricle magnesium supplementation combined with intracarotid magnesium supplementation combined with selective hypothermia.