Analysis of the effect of cations on protein conformational stability using solid-state nanopores.

The conformation of proteins is closely related to their biological functions, and it is affected by many factors, including the type of cations in solution. However, it is difficult to detect the conformational changes of a protein in situ. As a single-molecule sensing technology, nanopores can convert molecular structural information into analyzable current signals within a reasonable time range. Herein, we detect and analyze the effects of two different types of monovalent cations (Na+ and Li+) on a model protein bovine serum albumin (BSA) conformation using SiNx nanopores with different diameters. The quantitative analysis results show that the excluded volume of BSA in LiCl salt solutions is larger than the value in NaCl solution, indicating that Li+ is more prone to unfolding the proteins and making them unstable. This study demonstrated that nanopores enable the in situ detection of the structure of proteins at the single-molecule level and provide a new approach for the quantitative analysis of proteins.

Preoperative prediction of rectal Cancer staging combining MRI deep transfer learning, radiomics features, and clinical factors: accurate differentiation from stage T2 to T3.

BACKGROUND: This study evaluates the efficacy of integrating MRI deep transfer learning, radiomic signatures, and clinical variables to accurately preoperatively differentiate between stage T2 and T3 rectal cancer. METHODS: We included 361 patients with pathologically confirmed stage T2 or T3 rectal cancer, divided into a training set (252 patients) and a test set (109 patients) at a 7:3 ratio. The study utilized features derived from deep transfer learning and radiomics, with Spearman rank correlation and the Least Absolute Shrinkage and Selection Operator (LASSO) regression techniques to reduce feature redundancy. Predictive models were developed using Logistic Regression (LR), Random Forest (RF), Decision Tree (DT), and Support Vector Machine (SVM), selecting the best-performing model for a comprehensive predictive framework incorporating clinical data. RESULTS: After removing redundant features, 24 key features were identified. In the training set, the area under the curve (AUC)values for LR, RF, DT, and SVM were 0.867, 0.834, 0.900, and 0.944, respectively; in the test set, they were 0.847, 0.803, 0.842, and 0.910, respectively. The combined model, using SVM and clinical variables, achieved AUCs of 0.946 in the trainingset and 0.920 in the test set. CONCLUSION: The study confirms the utility of a combined model of MRI deep transfer learning, radiomic features, and clinical factors for preoperative classification of stage T2 vs. T3 rectal cancer, offering significant technological support for precise diagnosis and potential clinical application.

Carbon availability and microbial activity manipulate the temperature sensitivity of anaerobic degradation in a paddy soil profile.

Soil contains a substantial amount of organic carbon, and its feedback to global warming has garnered widespread attention due to its potential to modulate atmospheric carbon (C) storage. Temperature sensitivity (Q10) has been widely utilized as a measure of the temperature-induced enhancement in soil organic carbon (SOC) decomposition. It is currently rare to incorporate Q10 of CO2 and CH4 into the study of waterlogged soil profiles and explore the possibility of artificially reducing Q10 in rice fields. To investigate the key drivers of Q10, we collected 0-1 m paddy soil profiles, and stratified the soil for submerged anaerobic incubation. The relationship between SOC availability, microbial activity, and the Q10 of CO2 and CH4 emissions was examined. Our findings indicate that as the soil layer deepens, soil C availability and microbial activity declined, and the Q10 of anaerobic degradation increased. Warming increased C availability and microbial activity, accompanied by weakened temperature sensitivity. The Q10 of CO2 correlated strongly with soil resistant C components, while the Q10 of CH4 was significantly influenced by labile substrates. The temperature sensitivity of CH4 (Q10 = 3.99) was higher than CO2 emissions (Q10 = 1.78), indicating the need for greater attention of CH4 in predicting warming's impact on anaerobic degradation in rice fields. Comprehensively assessing CO2 and CH4 emissions, the 20-40 cm subsurface soil is the most temperature-sensitive. Despite being a high-risk area for C loss and CH4 emissions, management of this soil layer in agriculture has the potential to reduce the threat of global warming. This study underscores the importance of subsurface soil in paddy fields, advocating greater attention in scientific simulations and predictions of climate change.

Pseudomonas weihenstephanensis through the iron metabolism pathway promotes in situ spoilage capacity of prepared beef steaks during cold storage.

In this study, we evaluated the histomorphology, reactive oxygen species (ROS), protein degradation, and iron metabolism characteristics and differential expression analysis of genes for siderophores synthesis and protease secretion in prepared beef steaks inoculated alone or co-inoculated with P. weihenstephanensis, B. thermotrichothrix and M. caseolyticus at 4 °C for 12 days. The results showed that the P. weihenstephanensis was the key bacteria that degraded protein in the process of prepared beef steaks spoilage, which led to protein oxidation by promoting ferritin degradation to release free iron and inducing ROS accumulation. The highest expression of FpvA and AprE was detected in the P. weihenstephanensis group by comparing qRT-PCR of the different inoculation groups. Both qRT-PCR and Western blot revealed that ferritin heavy polypeptide and ferritin light chain polypeptide gene and protein expressions were significantly higher in the P. weihenstephanensis inoculation group compared to the other inoculation groups. Results suggested that FpvA and AprE might play roles in meat spoilage and were potential positional, physiological and functional candidate genes for improving the quality traits of prepared beef steaks. This work may provide insights on controlling food quality and safety by intervening in spoilage pathways targeting iron carrier biosynthesis or protease secretion genes.

Revealing the spoilage characteristics of refrigerated prepared beef steak by advanced bioinformatics tools.

BACKGROUND: Although microorganisms are the main cause of spoilage in prepared beef steaks, very few deep spoilage mechanisms have been reported so far. Aiming to unravel the mechanisms during 12 days of storage at 4 °C affecting the quality of prepared beef steak, the present study investigated the changes in microbial dynamic community using a combined high-throughput sequencing combined and bioinformatics. In addition, gas chromatography-mass spectrometry combined with multivariate statistical analysis was utilized to identify marker candidates for prepared steaks. Furthermore, cloud platform analysis was applied to determine prepared beef steak spoilage, including the relationship between microbiological and physicochemical indicators and volatile compounds. RESULTS: The results showed that the dominant groups of Pseudomonas, Brochothrix thermosphacta, Lactobacillus and Lactococcus caused the spoilage of prepared beef steak, which are strongly associated with significant changes in physicochemical properties and volatile organic compounds (furan-2-pentyl-, pentanal, 1-octanol, 1-nonanol and dimethyl sulfide). Metabolic pathways were proposed, among which lipid metabolism and amino acid metabolism were most abundant. CONCLUSION: The present study is helpful with respect to further understanding the relationship between spoilage microorganisms and the quality of prepared beef steak, and provides a reference for investigating the spoilage mechanism of dominant spoilage bacteria and how to extend the shelf life of meat products. © 2024 Society of Chemical Industry.

Optical coherence tomography parameters as prognostic factors for stereopsis after vitrectomy for unilateral epiretinal membrane: a cohort study.

This retrospective cohort study explored the relationship between monocular and interocular optical coherence tomography (OCT) parameters and stereopsis in 56 patients undergoing pars plana vitrectomy (PPV) for unilateral idiopathic epiretinal membrane (IERM). IERM impairs visual functions, with symptoms ranging from asymptomatic to severe impairment. Despite established surgical interventions, including PPV with membrane peeling, the impact on advanced three-dimensional visual functions such as stereopsis remains inadequately investigated. All subjects were assessed for stereopsis, visual acuity, and metamorphopsia, alongside spectral domain OCT parameters. These visual functions significantly improved 3-month postoperatively. Central retinal thickness at the fovea, parafovea, and perifovea (CFT, CRT-3 mm, and CRT-6 mm), ectopic inner foveal layer thickness, and retinal layer thickness notably decreased 1 week to 3 months after surgery. The interocular difference in OCT parameters between bilateral eyes was included as a parameter. Baseline CRT-3 mm difference and inner nuclear layer (INL) thickness were independently correlated with postoperative stereopsis on the Titmus Stereo Test, while baseline CRT-6 mm difference and INL thickness were independently related to stereopsis on the TNO stereotest. This study highlights the substantial enhancement in stereopsis post-IERM surgery, with both interocular and monocular OCT parameters independently influencing postoperative stereopsis. These findings underscore the importance of retinal microstructures in assessing and predicting stereopsis in IERM patients after vitrectomy.

The impact of preoperative parameters on postoperative foveal displacement in idiopathic macular hole.

This study examined the effect of vitrectomy combined with internal limiting membrane (ILM) peeling on foveal displacement in 42 eyes with idiopathic macular hole (IMH). A retrospective analysis was conducted to measure various macular hole parameters before surgery, including basal diameter, minimum diameter, hole height, and areas affected by traction such as macular hole area (MHA), macular hole cystoid space area (MHCSA), macular hole retinal area (MHRA), and total area (TA). The results showed a postoperative shift of the fovea towards the optic disc in all cases. Notably, the extent of foveal displacement was significantly linked to the preoperative basal diameter (rs = 0.405, P = 0.008) but not to other preoperative parameters or postoperative visual acuity. Furthermore, the study found that the temporal side of the macular hole was more affected by traction than the nasal side preoperatively, leading to greater postoperative displacement (All P < 0.05).

Retinal displacement after surgery for idiopathic macular hole.

AIM: To review and summarize the mechanism hypothesis, influencing factors and possible consequences of macular retinal displacement after idiopathic macular hole (IMH) surgery. METHODS: PubMed and Web of Science database was searched for studies published before April 2023 on "Retinal displacement", "Idiopathic macular holes", and "Macular displacement". RESULTS: Recently, more academics have begun to focus on retinal displacement following idiopathic macular holes. They found that internal limiting membrane (ILM) peeling was the main cause of inducing postoperative position shift in the macular region. Moreover, several studies have revealed that the macular hole itself, as well as ILM peeling method, will have an impact on the result. In addition, this phenomenon is related to postoperative changes in macular retinal thickness, cone outer segment tips line recovery, the occurrence of dissociated optic nerve fiber layer (DONFL) and the degree of metamorphopsia. CONCLUSION: As a subclinical phenomenon, the clinical significance of postoperative macular displacement cannot be underestimated as it may affect the recovery of anatomy and function.

Chitosan-based packaging films with antibacterial-sterilization integrated continuous activity for extending the shelf life of perishable foods.

The current food packaging films can be preservative but lack the function of combining antibacterial and sterilization which lead to films can not maximize prolong shelf life of perishable foods. This study provided a new strategy to realize prolonging shelf life of perishable foods by integrating antibacterial and sterilization which focused on applying photodynamic inactivation to films with continuous activity, where curcumin (CUR) and sodium copper chlorophyll (SCC) were loaded into chitosan (CS) films. Compared to pure CS films, the barrier capacity (oxygen permeability and water vapor permeability) and mechanical properties of composite films were improved by introducing CUR and SCC. In addition, the composite film can effectively against food-borne pathogenic bacteria and significantly prolong the shelf life of cherries and pork. The provided strategy has potential application prospects in food preservation packaging.

Total Biosynthesis of Circular Bacteriocins by Merging the Genetic Engineering and Enzymatic Catalysis.

Circular bacteriocins are known for their structural stability and effective antimicrobial properties, positioning them as potential natural food preservatives. However, their widespread application is impeded by restricted availability. This research developed a total biosynthesis platform for circular bacteriocins, with a focus on AS-48 by involving recombinant production of the linear precursor in Escherichia coli, followed by enzymatic cyclization of the precursor into cyclic AS-48 using the ligase butelase-1 in vitro. An important discovery is that, aside from fusion tags, the C-terminal motif LE and LEKKK also could affect the expression yield of the precursor. This biosynthesis platform is both versatile and high-yielding, achieving yields of 10-20 mg/L of AS-48. Importantly, the biosynthetic AS-48 exhibited a secondary structure and antimicrobial activities comparable to those of the native molecules. As such, this work proposes an effective synthetic approach for circular bacteriocins, facilitating their advancement and application in the food industry.

Effects of biodegradable microplastics and straw addition on soil greenhouse gas emissions.

Large pieces of plastic are transformed into microplastic particles through weathering, abrasion, and ultraviolet radiation, significantly impacting the soil ecosystem. However, studies on biodegradable microplastics replacing traditional microplastics as agricultural mulching films to drive the biogeochemical processes influenced by GHG are still in their initial stages, with limited relevant reports available. This study sought to investigate the effects of microplastic and straw addition on CO2 and N2O emissions in different soils. Herein, yellow-brown soil (S1) and fluvo-aquic soil (S2) were utilized, each treated with three different concentrations of PLA (polylactic acid) microplastics (0.25%, 2%, and 7% w/w) at 25 °C for 35 days, with and without straw addition. The results showed that straw (1% w/w) significantly increased soil CO2 by 4.1-fold and 3.2-fold, respectively, and N2O by 1.8-fold and 1.8-fold, respectively, in cumulative emissions in S1 and S2 compared with the control. PLA microplastics significantly increased CO2 emissions by 71.5% and 99.0% and decreased N2O emissions by 30.1% and 24.7% at a high concentration (7% w/w, PLA3) in S1 and S2 compared with the control, respectively. The same trend was observed with the addition of straw and microplastics together. Structural equation modeling and redundancy analysis confirmed that soil physiochemical parameters, enzyme and microbial activities are key factors regulating CO2 and N2O emissions. The addition of microplastics is equivalent to the addition of carbon sources, which can significantly affect DOC, MBC, SOC and the abundance of carbon-associated bacteria (CbbL), thereby increasing soil CO2 emissions. The addition of microplastics alone inhibited the activity of nitrogen cycling enzymes (urease activity), increasing the abundance of denitrifying microbes. However, adding a high amount of microplastics and straw together released plastic additives, inhibiting microbial abundance and reducing the nitrogen cycle. These effects decreased NH4+-N and increased NO3--N, resulting in decreased N2O emissions. This study indicates that biodegradable microplastics could reduce soil plastic residue pollution through degradation. However, their use could also increase CO2 emissions and decrease N2O emissions. Consequently, this research lays the groundwork for further investigation into the implications of utilizing biodegradable microplastics as agricultural mulch, particularly concerning soil geochemistry and GHG emissions.

Microfluidic synthesis of hemin@ZIF-8 nanozyme with applications in cellular reactive oxygen species detection and anticancer drug screening.

Zeolitic imidazolate framework-8 (ZIF-8) encapsulating enzymatically active biomolecules has emerged as a novel biocompatible nanozyme and offers significant implications for bioanalysis of various biomarkers towards early diagnosis of severe diseases such as cancers. However, the rapid, continuous and scalable synthesis of these nanozymes still remains challenging. In this work, we proposed a novel microfluidic approach for rapid and continuous synthesis of hemin@ZIF-8 nanozyme. By employing a distinctive combination of zigzag-shaped channel and spiral channel with sudden expansion structures, we have enhanced the mixing efficiency within the chip and achieved effective encapsulation of hemin in ZIF-8. The resulting hemin@ZIF-8 nanoparticles exhibit peroxidase-like activity and are capable of detecting free H2O2 with a limit of detection (LOD) as low as 45 nM, as well as H2O2 secreted by viable cells with a detection threshold of approximately 10 cells per mL. By leveraging this method, we achieved successful detection of cancer cells and effective screening of anticancer drugs that induce oxidative stress injury in cancer cells. This innovative microfluidic strategy offers a new avenue for synthesizing functional nanocomposites to facilitate the development of next-generation diagnostic tools for early disease detection and personalized medicine.

"Top-down" overexpression optimization of butelase-1 in Escherichia coli and its application in anti-tumor peptides.

Butelase-1, the fastest known Asn/Asp-specific peptide ligase capable of catalyzing peptide ligation and cyclization, holds promising application prospects in the fields of food and biology. However, limited research exists on its recombinant expression and potential applications in peptide drugs. In this study, the activity of recombinantly-produced butelase-1 was enhanced by co-expressing it with a molecular chaperone in the SHuffle T7 strain. By introducing single or multiple synonymous rare codons at the beginning of the coding regions of beta-strand or alpha-helix, in combination with ribosomal binding site engineering, the activity of butelase-1 could be further improved. Consequently, the butelase-1 with a specific activity of 386.93 U/mg and a catalytic efficiency of 11,048 M-1 s-1 was successfully prepared in E. coli, resulting in a total activity of 8183.54 U/L and a yield of about 100 mg/L. This optimized butelase-1 was then used to efficiently cyclize the redesigned anti-cancer peptide lunasin, leading to enhanced bioavailability and anti-cancer effects. Overall, this study not only provided valuable biotechnology strategies for improving the recombinant expression of butelase-1 but also demonstrated a successful application for enhancing the biological efficacy of anti-cancer peptides.