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Nature Communications Jun 2024Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water...
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.
Topics: Nanostructures; Polymers; Molecular Dynamics Simulation; Proteins; Models, Molecular; Solvents; Computational Biology; Software
PubMed: 38937468
DOI: 10.1038/s41467-024-49700-4 -
Nature Communications Jun 2024Developing superporous hemostatic sponges with simultaneously enhanced permeability and mechanical properties remains challenging but highly desirable to achieve rapid...
Developing superporous hemostatic sponges with simultaneously enhanced permeability and mechanical properties remains challenging but highly desirable to achieve rapid hemostasis for non-compressible hemorrhage. Typical approaches to improve the permeability of hemostatic sponges by increasing porosity sacrifice mechanical properties and yield limited pore interconnectivity, thereby undermining the hemostatic efficacy and subsequent tissue regeneration. Herein, we propose a temperature-assisted secondary network compaction strategy following the phase separation-induced primary compaction to fabricate the superporous chitosan sponge with highly-interconnected porous structure, enhanced blood absorption rate and capacity, and fatigue resistance. The superporous chitosan sponge exhibits rapid shape recovery after absorbing blood and maintains sufficient pressure on wounds to build a robust physical barrier to greatly improve hemostatic efficiency. Furthermore, the superporous chitosan sponge outperforms commercial gauze, gelatin sponges, and chitosan powder by enhancing hemostatic efficiency, cell infiltration, vascular regeneration, and in-situ tissue regeneration in non-compressible organ injury models, respectively. We believe the proposed secondary network compaction strategy provides a simple yet effective method to fabricate superporous hemostatic sponges for diverse clinical applications.
Topics: Animals; Porosity; Chitosan; Hemostatics; Swine; Hemostasis; Permeability; Hemorrhage; Male
PubMed: 38937462
DOI: 10.1038/s41467-024-49578-2 -
Nature Communications Jun 2024Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value...
Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this "red body," focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.
Topics: Cell Wall; Stramenopiles; Plastids
PubMed: 38937455
DOI: 10.1038/s41467-024-49277-y -
Cell Death & Disease Jun 2024In eukaryotes, the nucleolus is the critical non-membranous organelle within nuclei that is responsible for ribosomal DNA (rDNA) transcription and ribosome biogenesis....
In eukaryotes, the nucleolus is the critical non-membranous organelle within nuclei that is responsible for ribosomal DNA (rDNA) transcription and ribosome biogenesis. The transcription of rDNA, a rate-limiting step for ribosome biogenesis, is tightly regulated to meet the demand for global protein synthesis in response to cell physiology, especially in neurons, which undergo rapid changes in morphology and protein composition during development and synaptic plasticity. However, it is unknown how the pre-initiation complex for rDNA transcription is efficiently assembled within the nucleolus in neurons. Here, we report that the nucleolar protein, coronin 2B, regulates rDNA transcription and maintains nucleolar function through direct interaction with upstream binding factor (UBF), an activator of RNA polymerase I transcriptional machinery. We show that coronin 2B knockdown impairs the formation of the transcription initiation complex, inhibits rDNA transcription, destroys nucleolar integrity, and ultimately induces nucleolar stress. In turn, coronin 2B-mediated nucleolar stress leads to p53 stabilization and activation, eventually resulting in neuronal apoptosis. Thus, we identified that coronin 2B coordinates with UBF to regulate rDNA transcription and maintain proper nucleolar function in neurons.
Topics: Apoptosis; Cell Nucleolus; Neurons; Animals; Pol1 Transcription Initiation Complex Proteins; Humans; DNA, Ribosomal; Microfilament Proteins; Transcription, Genetic; Tumor Suppressor Protein p53; Mice; Stress, Physiological
PubMed: 38937439
DOI: 10.1038/s41419-024-06852-x -
Aging Jun 2024The primary objective of this study was to assess the diagnostic potential of galectin-3 (Gal-3), fractalkine (FKN), interleukin (IL)-6, microRNA(miR)-21, and cardiac...
OBJECTIVE
The primary objective of this study was to assess the diagnostic potential of galectin-3 (Gal-3), fractalkine (FKN), interleukin (IL)-6, microRNA(miR)-21, and cardiac troponin I (cTnI) in patients with ischemic cardiomyopathy (ICM).
METHOD
A total of 78 ICM patients (Case group) and 80 healthy volunteers (Control group) admitted to our hospital for treatment or physical examination from Aug. 2018 to Feb. 2020 were included in the current study. The serum concentration of Gal-3, FKN, IL-6, miR-21, and plasma expression of cTnI of both groups were determined. The severity of ICM was classified using New York Heart Association (NYHA) scale.
RESULTS
When compared with the control group, the case group had a significantly high blood concentration of Gal-3, FKN, IL-6, miR-21, and cTnI ( < 0.001). NYHA class II patients had lower blood levels of Gal-3, FKN, IL-6, miR-21, and cTnI than that in patients of NYHA class III and IV without statistical significance ( > 0.05). However, statistical significance could be achieved when comparing the above-analyzed markers in patients classified between class III and IV. Correlation analysis also revealed that serum levels of Gal-3, FKN, IL-6, miR-21, and cTnI were positively correlated with NYHA classification (R = 0.564, 0.621, 0.792, 0.981, < 0.05).
CONCLUSION
Our study revealed that up-regulated serum Gal-3, FKN, IL-6, miR-21, and cTnI levels were closely related to the progression of ICM. This association implies that these biomarkers have diagnostic potential, offering a promising avenue for early detection and monitoring of ICM progression.
Topics: Humans; Female; Male; Troponin I; Interleukin-6; MicroRNAs; Chemokine CX3CL1; Middle Aged; Galectin 3; Biomarkers; Aged; Myocardial Ischemia; Cardiomyopathies; Case-Control Studies; Galectins; Blood Proteins
PubMed: 38935941
DOI: 10.18632/aging.205953 -
PloS One 2024Colorectal cancer (CRC) is the third most common malignancy cause of cancer-related mortality worldwide. Epithelial-mesenchymal transition (EMT) promotes cancer...
Colorectal cancer (CRC) is the third most common malignancy cause of cancer-related mortality worldwide. Epithelial-mesenchymal transition (EMT) promotes cancer metastasis and a tumour-based Glasgow EMT score was associated with adverse clinical features and poor prognosis. In this study, the impact of using the established five tumour-based EMT markers consisting of E-cadherin (E-cad), β-catenin (β-cat), Snail, Zeb-1, and Fascin in combination with the stromal periostin (PN) on the prediction of CRC patients' prognosis were invesigated. Formalin-fixed paraffin-embedded tissues of 202 CRC patients were studies the expressions of E-cad, β-cat, Snail, Zeb-1, Fascin, and PN by immunohistochemistry. Individually, cytoplasmic Fascin (Fc), cytoplasmic Snail (Sc), nuclear Snail (Sn), stromal Snail (Ss), and stromal PN (Ps) were significantly associated with reduced survival. A combination of Ps with Fc, Fs, and Sn was observed in 2 patterns including combined Fc, Fs, and Ps (FcFsPs) and Fc, Sn, and Ps (FcSnPs). These combinations enhanced the prognostic power compared to individual EMT markers and were independent prognostic markers. As the previously established scoring method required five markers and stringent criteria, its clinical use might be limited. Therefore, using these novel combined prognostic markers, either FcFsPs or FcSnPs, may be useful in predicting CRC patient outcomes.
Topics: Humans; Colorectal Neoplasms; Snail Family Transcription Factors; Cell Adhesion Molecules; Prognosis; Female; Male; Middle Aged; Carrier Proteins; Microfilament Proteins; Epithelial-Mesenchymal Transition; Aged; Biomarkers, Tumor; Adult; Cadherins; Transcription Factors; beta Catenin; Aged, 80 and over; Periostin
PubMed: 38935747
DOI: 10.1371/journal.pone.0304666 -
Indian Journal of Dental Research :... Jan 2024Wet oral environment may have deleterious effects on performance of the composites due to influences of water sorption and solubility. The study evaluated the hydrolytic...
INTRODUCTION
Wet oral environment may have deleterious effects on performance of the composites due to influences of water sorption and solubility. The study evaluated the hydrolytic degradation caused because of water sorption and solubility of silorane and methacrylate-based dental composites.
METHODS
Ten disc samples (2 mm × 10 mm) were prepared. Samples were analyzed for water solubility and sorption according to ISO 4049:2000 regulations and tested for mass gain or loss following immersion in water or in artificial saliva at 1 day, 15 days, and 30 days period. Student's 't' test, repeated measures analysis of variance (ANOVA), and Tukey's post-hoc tests determined statistical significance of the experimental results with global significance set at P = 0.05.
RESULTS
Considerable sorption and solubility was observed with time in both materials on immersion. Silorane composites showed lower water sorption and solubility than methacrylate-based composite (MBC). Artificial saliva demonstrated higher sorption and solubility compared to distilled water.
CONCLUSION
Silorane composites display enhanced hydrolytic stability even after a month of immersion in contrast to conventional methacrylate-based composites (MBCs), making it a better alternative to MBC resins clinically.
Topics: Solubility; Methacrylates; Composite Resins; Water; Silorane Resins; Saliva, Artificial; Materials Testing; Hydrolysis; Dental Materials
PubMed: 38934754
DOI: 10.4103/ijdr.ijdr_195_23 -
Indian Journal of Dental Research :... Jan 2024The application of direct current can have a significant impact on the rate of tooth movement and surrounding periodontal ligament collagen turnover. This study aims to... (Comparative Study)
Comparative Study
An Immunohistochemical and Histological Study of the Animal Periodontal Ligament During Orthodontic Force Application with Concomitant Application of Electric Current - An Animal Study.
INTRODUCTION
The application of direct current can have a significant impact on the rate of tooth movement and surrounding periodontal ligament collagen turnover. This study aims to provide insight into the optimal characteristics of applied current to achieve enhanced tissue response.
METHOD
Eighteen male Wistar rats were divided into three groups (I, II, and III). Split mouth design was used, and each side was allocated into an experimental group or control group. Experimental sides of groups I, II, and III received 20, 10, and 15 μA of current (15 min, twice daily for 3 days). Both the experimental and control groups receive an orthodontic force via the NiTi closed coil spring. The amount of tooth movement was determined daily. Immunohistochemistry slides were scored using the immunoreactive scoring (IRS) system for collagen types I and III. One-way Analysis of Variance (ANOVA) and Tukey post hoc test were used to analyse the rate of tooth movement, while Mann-Whitney test was used to analyse IRS distribution between control and experimental groups.
RESULTS
Compared with the control group, there was a statistically significant difference in tooth movement in all the experimental groups, with group 3 showing the maximum rate on days 2 and 3. This was supported by immunoreactive scores for both collagen types I and III.
CONCLUSIONS
After 72 hours, the expression of collagen types 1 and 3 increased significantly for group III. This finding was in harmony with the rate of tooth movement, which was maximum for group 3 (15 μA) as compared to other groups.
Topics: Periodontal Ligament; Animals; Rats, Wistar; Tooth Movement Techniques; Male; Rats; Collagen Type I; Immunohistochemistry; Collagen Type III; Orthodontic Wires; Dental Alloys; Nickel; Stress, Mechanical; Titanium
PubMed: 38934753
DOI: 10.4103/ijdr.ijdr_905_22 -
Microbial Biotechnology Jun 2024Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a "living antibiotic"...
Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a "living antibiotic" in several fields such as agriculture or even medicine, since it is able to prey upon bacterial pathogens. Its interesting lifestyle makes this bacterium very attractive as a microbial chassis for co-culture systems including two partners. A limitation to this goal is the scarcity of suitable synthetic biology tools for predator domestication. To fill this gap, we have firstly adapted the hierarchical assembly cloning technique Golden Standard (GS) to make it compatible with B. bacteriovorus HD100. The chromosomal integration of the Tn7 transposon's mobile element, in conjunction with the application of the GS technique, has allowed the systematic characterization of a repertoire of constitutive and inducible promoters, facilitating the control of the expression of heterologous genes in this bacterium. PJ/EliR proved to be an exceptional promoter/regulator system in B. bacteriovorus HD100 when precise regulation is essential, while the synthetic promoter P showed a constitutive high expression. These genetic tools represent a step forward in the conversion of B. bacteriovorus into an amenable strain for microbial biotechnology approaches.
Topics: Synthetic Biology; Bdellovibrio bacteriovorus; Gene Expression Regulation, Bacterial; Promoter Regions, Genetic; DNA Transposable Elements; Cloning, Molecular; Recombinant Proteins
PubMed: 38934530
DOI: 10.1111/1751-7915.14517 -
Journal of Obstetrics and Gynaecology :... Dec 2024This study aimed to compare the tissue damage caused by barbed sutures and conventional sutures using scanning electron microscopy (SEM). Porcine myocardium was incised... (Comparative Study)
Comparative Study
This study aimed to compare the tissue damage caused by barbed sutures and conventional sutures using scanning electron microscopy (SEM). Porcine myocardium was incised and sutured using different thread types: barbed suture, (STRATAFIX Spiral PDS PLUS) and conventional sutures, (VICRYL and PDS Plus). Needle hole shapes were examined at magnifications of 30×-100×. VICRYL suture damaged the tissue and created large gaps around the needle holes. The tissue around the needle holes was smoother and less damaged in the single suture ligations with PDS; however, a large gap had formed. In the continuous suture with STRATAFIX, the tissue around the needle holes was significantly smoother and minimally damaged, with no noticeable gaps around the needle holes. Barbed sutures reduced the load on needle holes and minimised tissue damage owing to the dispersion of traction forces by the barbs compared with conventional sutures.
Topics: Animals; Sutures; Microscopy, Electron, Scanning; Swine; Suture Techniques; Models, Animal; Polyglactin 910; Myocardium
PubMed: 38934494
DOI: 10.1080/01443615.2024.2370973