Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis.

Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.

Quantification of ectopic fat storage in the liver and pancreas using six-point Dixon MRI and its association with insulin sensitivity and ß-cell function in patients with central obesity.

OBJECTIVES: To assess the association of ectopic fat deposition in the liver and pancreas quantified by Dixon magnetic resonance imaging (MRI) with insulin sensitivity and ß-cell function in patients with central obesity. MATERIALS AND METHODS: A cross-sectional study of 143 patients with central obesity with normal glucose tolerance (NGT), prediabetes (PreD), and untreated type 2 diabetes mellitus (T2DM) was conducted between December 2019 and March 2022. All participants underwent routine medical history taking, anthropometric measurements, and laboratory tests, including a standard glucose tolerance test to quantify insulin sensitivity and ß-cell function. The fat content in the liver and pancreas was measured with MRI using the six-point Dixon technique. RESULTS: Patients with T2DM and PreD had a higher liver fat fraction (LFF) than those with NGT, while those with T2DM had a higher pancreatic fat fraction (PFF) than those with PreD and NGT. LFF was positively correlated with homeostatic model assessment of insulin resistance (HOMA-IR), while PFF was negatively correlated with homeostatic model assessment of insulin secretion (HOMA-ß). Furthermore, using a structured equation model, we found LFF and PFF to be positively associated with glycosylated hemoglobin via HOMA-IR and HOMA-ß, respectively. CONCLUSIONS: In patients with central obesity, the effects of LFF and PFF on glucose metabolism. were associated with HOMA-IR and HOMA-ß, respectively. Ectopic fat storage in the liver and pancreas quantified by MR Dixon imaging potentially plays a notable role in the onset ofT2DM. CLINICAL RELEVANCE STATEMENT: We highlight the potential role of ectopic fat deposition in the liver and pancreas in the development of type 2 diabetes in patients with central obesity, providing valuable insights into the pathogenesis of the disease and potential targets for intervention. KEY POINTS: • Ectopic fat deposition in the liver and pancreas is associated with T2DM. • T2DM and prediabetes patients had higher liver and pancreatic fat fractions than normal individuals. • The results provide valuable insights into pathogenesis of T2DM and potential targets for intervention.

Applications of Hydrogels in Drug Delivery for Oral and Maxillofacial Diseases.

Oral and maxillofacial diseases have an important impact on local function, facial appearance, and general health. As a multifunctional platform, hydrogels are widely used in the biomedical field due to their excellent physicochemical properties. In recent years, a large number of studies have been conducted to adapt hydrogels to the complex oral and maxillofacial environment by modulating their pore size, swelling, degradability, stimulus-response properties, etc. Meanwhile, many studies have attempted to use hydrogels as drug delivery carriers to load drugs, cytokines, and stem cells for antibacterial, anticancer, and tissue regeneration applications in oral and maxillofacial regions. This paper reviews the application and research progress of hydrogel-based drug delivery systems in the treatment of oral and maxillofacial diseases such as caries, endodontic diseases, periodontal diseases, maxillofacial bone diseases, mucosal diseases, oral cancer, etc. The characteristics and applications of hydrogels and drug-delivery systems employed for the treatment of different diseases are discussed in order to provide a reference for further research on hydrogel drug-delivery systems in the future.

Roles of the cytoskeleton in human diseases.

Recently, researches have revealed the key roles of the cytoskeleton in the occurrence and development of multiple diseases, suggesting that targeting the cytoskeleton is a viable approach for treating numerous refractory diseases. The cytoskeleton is a highly structured and complex network composed of actin filaments, microtubules, and intermediate filaments. In normal cells, these three cytoskeleton components are highly integrated and coordinated. However, the cytoskeleton undergoes drastic remodeling in cytoskeleton-related diseases, causing changes in cell polarity, affecting the cell cycle, leading to senescent diseases, and influencing cell migration to accelerate cancer metastasis. Additionally, mutations or abnormalities in cytoskeletal proteins and their related proteins are closely associated with several congenital diseases. Therefore, this review summarizes the roles of the cytoskeleton in cytoskeleton-related diseases as well as its potential roles in disease treatment to provide insights regarding the physiological functions and pathological roles of the cytoskeleton.

Effects of different physical factors on osteogenic differentiation.

Osteoblasts are essential for bone formation and can perceive external mechanical stimuli, which are translated into biochemical responses that ultimately alter cell phenotypes and respond to environmental stimuli, described as mechanical transduction. These cells actively participate in osteogenesis and the formation and mineralisation of the extracellular bone matrix. This review summarises the basic physiological and biological mechanisms of five different physical stimuli, i.e. light, electricity, magnetism, force and sound, to induce osteogenesis; further, it summarises the effects of changing culture conditions on the morphology, structure and function of osteoblasts. These findings may provide a theoretical basis for further studies on bone physiology and pathology at the cytological level and will be useful in the clinical application of bone formation and bone regeneration technology.

Insights into the Structure-Performance Relationship and Viscosity Reduction Performance of Recyclable Magnetic Fe/Zeolite for Crude Oil Aquathermolysis.

Elucidating the structure-performance relationship of zeolites and their synergy with metals for the catalytic aquathermolysis of crude oil is crucial for designing efficient catalysts. Herein, the structure-performance relationship between the magnetic Fe-loaded zeolite's physicochemical properties and aquathermolysis performance is mainly explored. First, the catalytic aquathermolysis performance of various porous materials (Y, ß, MCM-41, and ZSM-5 zeolites) was probed to investigate the effect of different topological structures on the viscosity reduction of heavy oil. Results showed that ZSM-5 has a favorable pore structure and acidity, and its viscosity reduction performance is 1.7-4.1 times those of other zeolites; therefore, it is more suitable as a carrier for aquathermolysis to reduce viscosity. Then, Fe substance (such as Fe2O3 and Fe3O4) was loaded onto the ZSM-5 support. It was found that Fe3O4/ZSM-5 had better performance compared with pure ZSM-5 and Fe2O3/ZSM-5, which could reduce the viscosity of heavy oil by 20.3%. Importantly, the Fe3O4/ZSM-5 catalyst is easily separated from crude oil due to its magnetism, hence it has the potential to be recycled and reused. In addition, the potential structure-performance relationship was systematically studied by X-ray diffraction (XRD), elemental analysis (EL), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FT-IR). As a result, it was considered that Fe3O4/ZSM-5 broke C-S bonds and reduced the heavy components (resin and asphaltene) of crude oil. This study has a certain guiding significance for developing heterogeneous magnetic hydrothermal viscosity reduction catalysts.

The lipoxygenase gene OsRCI-1 is involved in the biosynthesis of herbivore-induced JAs and regulates plant defense and growth in rice.

The pathway mediated by jasmonic acid (JA), biosynthesized via 13-lipoxygenases (LOX), plays a central role in both plant development and defense. In rice, there are at least fourteen 13-LOXs. Yet, only two 13-LOXs have been known to be involved in the biosynthesis of JA and plant defenses in rice. Here we cloned a chloroplast-localized 13-LOX gene from rice, OsRCI-1, whose transcripts were upregulated following infestation by brown planthopper (BPH, Nilaparvata lugens), one of the most important pests in rice. Overexpression of OsRCI-1 (oeRCI lines) increased levels of BPH-induced JA, jasmonate-isoleucine, trypsin protease inhibitors and three volatile compounds, 2-heptanone, 2-heptanol and α-thujene. BPHs showed a decreased colonization, fecundity and mass, and developed slowly on oeRCI plants compared with wild-type (WT) plants. Moreover, BPH-infested oeRCI plants were more attractive to the egg parasitoid of BPH, Anagrus nilaparvatae than equally treated WT plants. The decreased attractiveness to BPH and enhanced attractiveness to the parasitoid of oeRCI plants correlated with higher levels of BPH-induced 2-heptanone and 2-heptanol, and 2-heptanone, respectively. Compared with oeRCI plants, WT plants had higher plant height and 1000-grain weight. These results indicate that OsRCI-1 is involved in herbivore-induced JA bursts and plays a role in plant defense and growth.

Recent Research on Hybrid Hydrogels for Infection Treatment and Bone Repair.

The repair of infected bone defects (IBDs) is still a great challenge in clinic. A successful treatment for IBDs should simultaneously resolve both infection control and bone defect repair. Hydrogels are water-swollen hydrophilic materials that maintain a distinct three-dimensional structure, helping load various antibacterial drugs and biomolecules. Hybrid hydrogels may potentially possess antibacterial ability and osteogenic activity. This review summarizes the recent progress of different kinds of antibacterial agents (including inorganic, organic, and natural) encapsulated in hydrogels. Several representative hydrogels of each category and their antibacterial mechanism and effect on bone repair are presented. Moreover, the advantages and disadvantages of antibacterial agent hybrid hydrogels are discussed. The challenge and future research directions are further prospected.

Biodegradation of 4-hydroxybenzoic acid by Acinetobacter johnsonii FZ-5 and Klebsiella oxytoca FZ-8 under anaerobic conditions.

4-Hydroxybenzoic acid (4-HBA) is a common organic compound that is prevalent in the environment, and the persistence of 4-HBA residues results in exertion of pollution-related detrimental effects. Bioremediation is an effective method for the removal of 4-HBA from the environment. In this study, two bacterial strains FZ-5 and FZ-8 capable of utilizing 4-HBA as the sole carbon and energy source under anaerobic conditions were isolated from marine sediment samples. Phylogenetic analysis identified the two strains FZ-5 and FZ-8 as Acinetobacter johnsonii and Klebsiella oxytoca, respectively. The strains FZ-5 and FZ-8 degraded 2000 mg·L-1 4-HBA in 72 h with degradation rates of 71.04% and 80.10%, respectively. The optimum culture conditions for degradation by the strains and crude enzymes were also investigated. The strains FZ-5 and FZ-8 also exhibited the ability to degrade other lignin-derived compounds, such as protocatechuic acid, cinnamic acid, and vanillic acid. Immobilization of the two strains showed that they could be used for the bioremediation of 4-HBA in an aqueous environment. Soils inoculated with the strains FZ-5 and FZ-8 showed higher degradation of 4-HBA than the uninoculated soil, and the strains could survive efficiently in anaerobic soil. This is the first report of 4-HBA-degrading bacteria, belonging to the two genera, which showed degradation ability under anaerobic conditions. This study expound the strains could efficiently degrade 4-HBA in anaerobic soil and will help in the development of 4-HBA anaerobic bioremediation systems.

Correction: Isolation and characterization marine bacteria capable of degrading lignin-derived compounds.

[This corrects the article DOI: 10.1371/journal.pone.0240187.].

DNA methylation detection technology and plasma-based methylation biomarkers in screening of gastrointestinal carcinoma.

DNA methylation is of paramount importance for the evolution of human cancers. Its high sensitivity and specificity make it a potential biomarker for early cancer screening in the context of an increasing global burden of gastrointestinal (GI) carcinoma. More DNA methylation biomarkers are emerging with the development of liquid biopsy and sensitive DNA methylation detection technology. This review provides an overview of DNA methylation, focusing on the presentation and comparison of 5-methylcytosine detection technologies, and introduces the promising plasma-based cell-free DNA (cfDNA) methylation biomarkers published in recent years for early screening of GI carcinoma. Finally, we summarize and discuss the future of plasma cfDNA methylation markers detection as a clinical tool for early screening of GI carcinoma.

Lay abstract In the context of an increasing global burden of gastrointestinal (GI) carcinoma, early cancer screening is of paramount importance, so there is an urgent need for efficient and reliable potential biomarkers. More biomarkers are emerging with the development of noninvasive test and related detection technologies. This review provides an overview of certain potential biomarkers named DNA methylation, focusing on the presentation and comparison of related detection technologies for this type of biomarkers and introduces the promising plasma-based biomarkers published in recent years for early screening of GI carcinoma. Finally, we summarize and discuss the future of plasma-based biomarkers detection as a clinical tool for early screening of GI carcinoma.

Molecular testing for H. pylori clarithromycin and quinolone resistance: a prospective Chinese study.

In China, there is a high prevalence of antibiotic-resistant Helicobacter pylori infections in the population. The aim of the study was to assess a new ARMS-PCR test for detection of H. pylori clarithromycin resistance (CR) and quinolone resistance (QR) mutations and evaluate the spectrum of antibiotic resistance in patients from three Chinese provinces. Sanger sequencing and multiplex ARMS-PCR were used to detect H. pylori CR and QR bacteria in gastric biopsy samples. Among the 1,182 patients enrolled with gastritis, 643 (54.4%) were positive for H. pylori. Of these, 371 (57.7%) had antibiotic-resistant strains, comprising 236 (63.6%) with a single drug antibiotic-resistant strain and 135 (36.4%) with multiple drug-resistant strains. Following Sanger sequencing analysis of 23S rRNA and gyrA gene for mutations (antibiotic resistance markers), rates of CR, QR, and multidrug resistance (CR and QR) were 19.9, 12.0, and 25.8%, respectively. The 23S rRNA CR mutation A2143G (286, 96.9%) and the gyrA QR mutations C261A (85, 31.5%) and G271A (71, 26.3%) were common. Benchmarking against Sanger sequencing results, multiplex ARMS-PCR test had a high diagnostic sensitivity and specificity for detection of CR (96 and 93%), QR (95 and 92%) and multidrug resistance (95 and 95%). Based on our findings, the high incidence of single and multiple antibiotic resistance requires the routine checking of antibiotic resistance in all patients with suspected H. pylori infections. Multiplex ARMS-PCR is a simple and rapid test that can be now used for more efficient treatment of H. pylori infections and reduces the misuse of antibiotics.

Isolation and characterization marine bacteria capable of degrading lignin-derived compounds.

Lignin, a characteristic component of terrestrial plants. Rivers transport large amounts of vascular plant organic matter into the oceans where lignin can degrade over time; however, microorganisms involved in this degradation have not been identified. In this study, several bacterial strains were isolated from marine samples using the lignin-derived compound vanillic acid (4-hydroxy-3-methoxybenzoic acid) as the sole carbon and energy source. The optimum growth temperature for all isolates ranged from 30 to 35°C. All isolates grew well in a wide NaCl concentration range of 0 to over 50 g/L, with an optimum concentration of 22.8 g/L, which is the same as natural seawater. Phylogenetic analysis indicates that these strains are the members of Halomonas, Arthrobacter, Pseudoalteromonas, Marinomonas, and Thalassospira. These isolates are also able to use other lignin-derived compounds, such as 4-hydroxybenzoic acid, ferulic acid, syringic acid, and benzoic acid. Vanillic acid was detected in all culture media when isolates were grown on ferulic acid as the sole carbon source; however, no 4-hydroxy-3-methoxystyrene was detected, indicating that ferulic acid metabolism by these strains occurs via the elimination of two side chain carbons. Furthermore, the isolates exhibit 3,4-dioxygenase or 4,5-dioxygenase activity for protocatechuic acid ring-cleavage, which is consistent with the genetic sequences of related genera. This study was conducted to isolate and characterize marine bacteria of degrading lignin-derived compounds, thereby revealing the degradation of aromatic compounds in the marine environment and opening up new avenues for the development and utilization of marine biological resources.