Frontiers in systems biology最新文献

miRNAs are promising diagnostic biomarkers. These small RNA molecules are always present in the human body but become dysregulated when a person develops certain diseases. Although the detection of these biomarkers in cell-free tests is ongoing work, current systems often focus solely on detecting the presence or absence of a specific miRNA, rather than the miRNAs concentration. Thus, these tests may miss relative changes in miRNA concentration when disease-induced dysregulation occurs. This work, part of the WUR iGEM 2024 project (miRADAR), aimed to address this gap by incorporating an miRNA concentration-dependent threshold mechanism in a cell-free diagnostic test. In this system, continuous miRNA input concentrations need to be converted into a binary output signal, classifying the miRNA concentration as healthy (no output signal) or indicative of disease (strong output signal). To aid the experimental engineering of the test, here we use mathematical models to evaluate and assess different candidate networks. We apply a previously published multi-objective optimisation strategy to obtain designs that satisfy relevant constraints, such as low basal expression, high readout levels, and steep switching behaviour between low and high input miRNA concentrations. Models for three different biological mechanisms were compared based on their ability to generate the desired binary output signal. One approach used three-node protein networks (such as feed-forward loops), while the other two utilised RNA-based toehold systems. Overall, the toehold-mediated strand displacement systems demonstrated the most potential for experimental implementation. These systems are believed to be less burdensome in a cell-free environment, can be more readily engineered for new miRNA sequences, and showed high detection accuracy. Based on our results, we discuss how the inclusion of sequence-specific parameters could expand the design space of our mathematical models and how careful engineering of optimisation criteria is required to evaluate designs. Ultimately, our model-based study highlights that toehold-mediated strand displacement networks have the potential to be efficient miRNA detection systems for biosensing tools in the future.

Irrational antibiotic use contributes to the development of antibiotic resistance in bacteria, which is a major cause of healthcare-associated infections globally. Molecular research has shown that multiple resistance frequently develops from the uptake of pre-existing resistance genes, which are subsequently intensified under selective pressures. Resistant genes spread and are acquired through mobile genetic elements which are essential for facilitating horizontal gene transfer. MGEs have been identified as carriers of genetic material and are a significant player in evolutionary processes. These include insertion sequences, transposons, integrative and conjugative elements, plasmids, and genomic islands, all of which can transfer between and within DNA molecules. With an emphasis on pathogenic bacteria, this review highlights the salient features of the MGEs that contribute to the development and spread of antibiotic resistance. MGEs carry non-essential genes, including AMR and virulence genes, which can enhance the adaptability and fitness of their bacterial hosts. These elements employ evolutionary strategies to facilitate their replication and dissemination, thus enabling survival without positive selection for the harboring of beneficial genes.

By 2050, global population growth will significantly increase food demand, placing additional pressure on agriculture, a sector already vulnerable to climate change. Traditional approaches like fertilizers and pesticides have helped boost yields but are increasingly seen as unsustainable. As bioengineering becomes more accessible, engineered soil microorganisms are emerging as promising alternatives. However, their application in the rhizosphere is often limited by poor survivability and the high metabolic cost of expressing heterologous genes without appropriate regulation. To address this, we developed a microbial whole-cell biosensor that activates gene expression only under favorable conditions: in close proximity to plant roots and at high bacterial population densities. We engineered the pSal/nahR system in our host Pseudomonas fluorescens SBW25 to respond to salicylic acid, a key root exudate. In parallel, we implemented a quorum sensing system based on LuxI and the luxpR/LuxR pair to monitor cell density. Both inputs were integrated using a toehold switch-based AND gate, triggering expression only when both conditions were met. This strategy minimizes metabolic burden and offers a tightly controlled system for expression at target locations. While further validation in rhizosphere-like conditions is required, our results provide a foundation for safer open-environment applications of microorganisms, making this biosensor a versatile tool for future agricultural biotechnology.

Introduction: Preterm hypoxic-ischemic encephalopathy (pHIE) is a complex brain injury that contributes to chronic neural inflammation and neurological disorders. The signs and symptoms of in utero pHIE can often be overlooked, untreated or lumped into more generic conditions such as encephalopathy of prematurity (EOP). Clinical interventions like hypothermia and erythropoietin do not improve pHIE. We characterized a murine model for pHIE, which includes hypoxia and maternal factors as a cost-effective alternative to large animal models of HIE.

Methods: We injected pregnant mouse dams with LPS to stimulate an inflammatory response on embryonic days 15-16 (E15-E16), and whole cage hypoxia exposures occurred from postnatal days 3 to 9. To quantify the development of inflammation in the pHIE model, we used immunohistochemistry to stain for Caspase-9 in the cortex (20 μm per slice) and then counted Caspase-9 positive cells using unbiased stereology. We stained brain tissue with MAP2 to quantify neuronal intermediate filament expression and staining using a machine-learning based image analysis approach. We quantified cytokines (IL-1β, IL-6, IL-10, IL-18 and TNF-α) using RT-qPCR and (IL-18) ELISA to characterize differential expression in all treatment groups. The pHIE animals were compared with controls (LPS-Normoxia, Saline-Hypoxia, Saline-Normoxia, and Naïve) and with a model of only hypoxia (10% O₂) exposure in mouse pups.

Results: The pHIE pups showed significantly higher expression of Caspase-9 throughout the cortex compared to Naïve pup brains (p < 0.05). MAP2 expression was significantly decreased (p < 0.05) between 1.5-6.0 mm of the brain compared to Saline-Hypoxia and Naïve animals. Both IL-1β and IL-10 expression in LPS-Hypoxia animals was significantly higher (p < 0.05) than in Saline-Hypoxia and Naive animals. TNF-α expression was not significantly different between LPS-Hypoxia and Saline-Hypoxia animals. However, both showed significantly different transcription, compared to Naive animals.

Discussion: The model we describe here shows cortical damage similar to that seen in human HIE.

Global textile manufacturing practices are responsible for an increasing amount of textile waste that pollutes our planet. Mixed fiber blends pose a recycling challenge due to their heterogeneous structure. Current mechanical, chemical, thermochemical and enzymatic strategies suffer from several limitations such as high energy costs, extensive pre-treatment requirements and enzyme instability. This mini-review aims to present recent developments in the research field and to introduce Spore Surface Display (SSD) technology as a new biological approach for mixed textile degradation. SSD allows enzymes to be anchored on the robust bacterial spore surface, immobilizing multiple enzymes required for simultaneous cotton-polyester degradation into their respective monomers. The mini-review also includes an initial proposal for a process design suitable for a full mixed textile degradation process using this synthetic biology approach.

Current evidence suggests sodium-glucose cotransporter 2 inhibitors (SGLT2i) do not consistently improve patient physical function, despite improvements in clinical symptoms and reductions in both adiposity and body weight. We highlight heterogenous methodologies in SGLT2i physical function trials. We then provide context to these findings by collating new data which describes how reduced glycaemia with SGLT2i alters numerous physiological processes and discuss how these alterations may diminish or prevent expected functional improvements. Alterations include changes to energy homeostasis, pancreatic hormones, muscle metabolism, physical activity, and appetite regulation. Current evidence in humans is limited and the mechanistic interaction between SGLT2i, skeletal muscle, and physical function remains incompletely understood. Future investigations must embed comprehensive molecular techniques within suitably designed clinical trials to determine how skeletal muscle health and patient mobility is influenced by acute and long term SGLT2i prescription.

Losartan is a selective angiotensin II AT1-receptor antagonist for the treatment of arterial hypertension and heart failure. It is converted to a pharmacologically active metabolite carboxylosartan (E-3174) in the liver mainly by CYP2C9 enzyme, a member of the cytochrome P450 superfamily. The gene encoding this protein is highly polymorphic: numerous single nucleotide polymorphisms that alter the enzyme function have been described in the literature. The most widespread CYP2C9 alleles are CYP2C9*1 (wild-type), CYP2C9*2, and CYP2C9*3. Here we performed mathematical modeling of the metabolism of orally administered losartan to E-3174 taking into account combinations of the most common CYP2C9 alleles. Next, using the previously created model of the human cardiovascular and renal systems, we demonstrated that the blood pressure response to losartan therapy in a cohort of virtual hypertensive patients depended on CYP2C9 allelic variants. Individuals with the CYP2C9*1/CYP2C9*1 genotype responded better to treatment than patients carrying CYP2C9*2 or CYP2C9*3 alleles. The results of the modeling can potentially be used for personalization of drug therapy for arterial hypertension.

Background: The increasing incidence of inflammatory bowel diseases (IBD) over the last two decades has prompted the need to create new types of therapeutic interventions. The gut microbiome has emerged as a key component in the prognosis and pathophysiology of IBDs. The alteration or dysbiosis of the gut microbiome has been shown to exacerbate IBDs. The bacterial composition of the gut microbiome can be modulated through the usage of probiotics, prebiotics, and synbiotics. These interventions induce the growth of beneficial bacteria. Additionally, these interventions could be used to maintain gut homeostasis, reduce the inflammation seen in these morbidities, and strengthen the gut epithelial barrier.

Methods: The literature review was conducted in October 2024 using PubMed, Scopus, and Google Scholar screening for recent clinical trials in addition to reviews relevant to the topic.

Aims: This review aims to summarize the recent clinical trials of probiotics, prebiotics, and synbiotics in IBD patients highlighting their potential benefits in alleviating symptoms and enhancing the quality of life.

Conclusion: Certain probiotic formulations such as single strain ones consisting of Lactobacillus, or mixed-strain combinations of Lactobacillus and Bifidobacterium, prebiotic compounds such as fructooligosaccharides, and synbiotic combinations of both have proven effective in improving the clinical, immunological, and symptomatic aspects of the disease course. While promising, these findings remain inconclusive due to inconsistent study designs, small sample sizes, and varying patient responses. This emphasizes the need for larger, well-controlled trials to determine their clinical efficacy.