Gel Analysis Research Articles

Stress-stress correlations reveal force chains in gels.

We investigate the spatial correlations of microscopic stresses in soft particulate gels using 2D and 3D numerical simulations. We use a recently developed theoretical framework predicting the analytical form of stress-stress correlations in amorphous assemblies of athermal grains that acquire rigidity under an external load. These correlations exhibit a pinch-point singularity in Fourier space. This leads to long-range correlations and strong anisotropy in real space, which are at the origin of force-chains in granular solids. Our analysis of the model particulate gels at low particle volume fractions demonstrates that stress-stress correlations in these soft materials have characteristics very similar to those in granular solids and can be used to identify force chains. We show that the stress-stress correlations can distinguish floppy from rigid gel networks and that the intensity patterns reflect changes in shear moduli and network topology, due to the emergence of rigid structures during solidification.

Repeated Application and Removal of Polyisocyanopeptide Hydrogel Wound Dressings in a Splinted Full-Thickness Wound Model.

Polyisocyanopeptide (PIC) hydrogels are proposed as promising wound dressings. These gels are thermo-sensitive, allow application as a cold liquid, and rely on gelation through body heat. It is supposed that the gel can be easily removed by reversing the gelation and washing it away with a cold irrigation solution. The impact on wound healing of the regular application and removal of PIC dressings is compared to a single application of PIC and the clinically used Tegaderm™ in murine splinted full-thickness wounds for up to 14 days. SPECT/CT analysis of 111In-labelled PIC gels showed that, on average, 58% of the PIC gel could be washed out of the wounds with the employed method, which is, however, heavily influenced by personal technique. Evaluation with photography and (immuno-)histology showed that wounds in which PIC dressings were regularly removed and replaced were smaller at 14 days post-injury but performed on par with the control treatment. Moreover, the encapsulation of PIC in wound tissue was less severe and occurred less often when PIC was regularly refreshed. In addition, no morphological damage related to the removal procedure was observed. Thus, PIC gels are atraumatic and perform similarly to currently employed wound dressing materials, offering possible future benefits for both clinicians and patients.

Leclercia adecarboxylata C12, The Newly Isolated Cellulose-degrading Bacteria from Indonesian Coffee Pulp

Culturable cellulose-degrading microorganisms were collected from Arabica coffee pulp in East Java, Indonesia. Fifty isolates were obtained, and thirty-three isolates showed hydrolyzing zone on Carboxy Methyl Cellulose agar plates after Congo-Red staining. The highest specific CMCase activity was observed by isolates C12, identified as Leclercia adecarboxylata based on 16S-rRNA gene sequence analysis. SDS-PAGE of Leclercia adecarboxylata C12 cellulase revealed two bands with a molecular mass of 95.49 and 81.28 kDa, respectively. Activity gel analysis showed the cellulolytic ability of Leclercia adecarboxylata C12 cellulase by clear zone formation. The optimal CMCase activity was achieved at 50°C and pH 9, and the activity retained 47% of its initial activity after incubation at 50°C for 90 minutes. The purified enzyme remains stable from pH 5 to 10, with 77% of its maximum activity. The activity of CMCase was stimulated by the presence of K+, Ca2+, Mg2+, and Fe3+, while SDS and EDTA reduced its activity. The current study shows that the thermostable-alkalophilic cellulase produced by Leclercia adecarboxylata C12 is very promising for industrial applications.

Mechanochemical devulcanization ofEPDMrubber waste. Correlation of process parameters with sol–gel analyses and revulcanization properties

AbstractEthylene–propylene–diene rubber (EPDM) scrap was devulcanized in an internal mixer with varying amounts of dibenzamido diphenyl disulfide (DBD) at temperatures below 200°C. The devulcanization effect and sol–gel analyses of the devulcanizates, and the mechanical properties of the sulfur‐cured revulcanizates were studied. Residual DBD was still present in the sol at 160°C and degraded DBD at 200°C. DBD affects the curing leading to poor properties. So, the temperature must be adjusted according to the DBD concentration to obtain a superior recyclate for sealing systems. At 0.4 wt% DBD, the degradation reaction was already complete at 120°C, but only 52% and 61% of the tensile strengthσand strain at breakεof the virgin material were achieved. At 160°C and 2 wt%, the degradation reaction was complete, and the DBD effect on properties was small; 65% and 86% ofσandεwere recovered, respectively. To prevent property degradation, 200°C was required at 3.9 wt% DBD, resulting in 97% and 95% ofσandε, but only 70% of hardness.

Proteomic Analysis of Pecan (Carya illinoinensis) Nut Development

Pecan (Carya illinoinensis) nuts are an economically valuable crop native to the United States and Mexico. A proteomic summary from two pecan cultivars at multiple time points was used to compare protein accumulation during pecan kernel development. Patterns of soluble protein accumulation were elucidated using qualitative gel-free and label-free mass-spectrometric proteomic analyses and quantitative (label-free) 2-D gel electrophoresis. Two-dimensional (2-D) gel electrophoresis distinguished a total of 1267 protein spots and shotgun proteomics identified 556 proteins. Rapid overall protein accumulation occurred in mid-September during the transition to the dough stage as the cotyledons enlarge within the kernel. Pecan allergens Car i 1 and Car i 2 were first observed to accumulate during the dough stage in late September. While overall protein accumulation increased, the presence of histones diminished during development. Twelve protein spots accumulated differentially based on 2-D gel analysis in the weeklong interval between the dough stage and the transition into a mature kernel, while eleven protein spots were differentially accumulated between the two cultivars. These results provide a foundation for more focused proteomic analyses of pecans that may be used in the future to identify proteins that are important for desirable traits, such as reduced allergen content, improved polyphenol or lipid content, increased tolerance to salinity, biotic stress, seed hardiness, and seed viability.

Chi sequences switch the RecBCD helicase–nuclease complex from degradative to replicative modes during the completion of DNA replication

Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase-nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with cross-over hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced-replication is processive, but uncoupled with respect to leading and lagging strand synthesis, and can be suppressed by ter sites which limit replisome progression. Our observations demonstrate that convergent replisomes create a substrate that is processed by RecBCD, and that chi, when encountered, switches RecBCD from a degradative to replicative function. We propose that chi serves to functionally differentiate DNA ends created during completion, which require degradation, from those created by chromosomal double-strand breaks, which require resynthesis.

Separation Properties of Plasmid DNA Using a Two-Stage Particle Adsorption-Microfiltration Process

Plasmid DNA is used as a vector for gene therapy and DNA vaccination; therefore, the establishment of a mass production method is required. Membrane filtration is widely employed as a separation method suitable for the mass production of plasmid DNA. Furthermore, the separation of plasmid DNA using microfiltration and ultrafiltration membranes is being investigated. Because plasmid DNA has a circular structure, it undergoes significant deformation during filtration and easily permeates the membrane, hindering the selection of separation membranes based on molecular weight. In this study, we applied affinity microfiltration to plasmid DNA purification. α-Fe2O3 with an isoelectric point of approximately 8 and a particle size of 0.5 μm was selected as the ligand for two-stage affinity microfiltration of plasmid DNA. In the first stage of microfiltration, the experiment was conducted at a pH of 5, and a cake of α-Fe2O3 with bound plasmid DNA was obtained. Next, liquid permeation (pH 9 and 10) through the cake was performed to elute the bound plasmid DNA. Plasmid DNA was eluted during the early phase of liquid permeation at pH 10. Furthermore, agarose gel analysis confirmed the usefulness of the two-stage affinity microfiltration method with adsorption and desorption for plasmid DNA purification.

Experimental preparation and mechanism analysis of a neotype composite gel for coal spontaneous combustion prevention and coal-fire extinguishment

Spontaneous coal combustion (SCC) seriously threatens the safety production of coal mines. A neoteric irreversibly thermo-sensitive composite gel based on konjac glucomannan (KGM) and expandable graphite (EG) was elaborately synthesized for preventing SCC disasters and coal fires. Firstly, the primary properties such as the gelation time, the water retention rate, the rheological law, the microstructure characteristics, and the thermal decomposition properties concerning the composite gel were explored systematically. The results demonstrated that composite gel is non-Newton fluids with excellent self-repairing capability, and the gel exhibited controllable gelation properties, favorable seepage capacity, and strong water retention characteristics. Besides, SEM observations and thermogravimetry analysis suggested that the interspersed network structures of KGM embedded by EG exhibits higher denseness, greater physical strength, superior structural stability, and more remarkable thermal stability, and EG was closely adhered to the KGM hydrogel network but distributed inhomogeneously. Furthermore, the high-temperature pyrolysis tests showed that the decomposition rate accelerated to 0.234 %/°C and 0.225 %/°C at the temperature of 266.5 °C and 275.1 °C, respectively. Meanwhile, both the low-temperature oxidation experiments and fire-extinguishing experiments showed a favorable inhibition effect of the composite KGM@EG gel, indicating that KGM@EG gel is applicable to inhibit the high-temperature pyrolysis rate of coal, and could effectively inhibit the heat buildup, O2 consumption, and CO formation over the oxidation and combustion process of coal, which would lower the possibility of SCC and coal fires. Therefore, KGM@EG composite gel can play an efficient SCC-preventing and fire-extinguishing role in the safety production of coal mines. Finally, the underlying mechanism for SCC preventing and fire-extinguishing concerning the thermo-sensitive gel was revealed and proposed.

Insulator-to-metal transition in RCoO3 (R = Pr, Nd)

We report a straightforward tool to investigate insulator-metal transition in RCo[Formula: see text] (R = Pr, and Nd) nanoparticles prepared by a sol–gel technique. Thermogravimetric analysis (TGA) of the as-prepared gel is performed to get the lowest possible calcination temperature of RCo[Formula: see text] nanoparticles. The Rietveld refinement of the powder X-ray diffraction (XRD) patterns for both samples shows that the samples crystallize in the orthorhombic (Pnma) phase at room temperature. The particle size of the sample is determined by scanning electron microscopy. Ac conductivity of the materials is analyzed in the temperature range from 303 K to 673 K and in the frequency range from 42 Hz to 1.1 MHz. The insulator-to-metal transition of PrCo[Formula: see text] and NdCo[Formula: see text] is analyzed by ac impedance spectroscopy. DC resistivity measurement is also done to cross check the insulator-metal transition in RCo[Formula: see text] system.

State of the Art of Hydrogel Wound Dressings Developed by Ionizing Radiation.

The development of an ideal hydrogel wound dressing with excellent characteristics is currently a significant demand in wound therapy. The ideal hydrogel wound dressing must provide a moist environment between the wound and the dressing, promote wound healing, absorb excess exudate and toxins, be completely sterile, and not adhere to the wound. The evolution and current status of research on hydrogel wound dressings obtained exclusively through production by ionizing radiation are discussed in this paper review, along with the preparation methods, properties, standard characterization techniques, and their applications in wound dressing. First, we described the methods for synthesizing hydrogel wound dressings with ionizing radiation. Then, standard methods of characterization of hydrogel wound dressings such as gel fraction, swelling degree, sol-gel analysis, rheological properties, morphology, moisture retention capability, and water vapor transmission rate have been investigated. In the end, specific attention was paid to the drug release, antibacterial performance, and cytotoxicity of hydrogels. Moreover, the application of hydrogel in regenerative medicine as wound healing dressing was covered.

Real-Time PCR Method for Assessment of ParA-Mediated Recombination Efficiency in Minicircle Production.

The in vivo intramolecular recombination of a parental plasmid allows excising prokaryotic backbone from the eukaryotic cassette of interest, leading to the formation of, respectively, a miniplasmid and a minicircle. Here we describe a real-time PCR protocol suitable for the determination of recombination efficiency of parental plasmids with multimer resolution sites (MRS). The protocol was successfully applied to purified DNA samples obtained from E. coli cultures, allowing a more reproducible determination of recombination efficiency than densitometry analysis of agarose gels.

Coconut-husk derived graphene for supercapacitor applications: comparative analysis of polymer gel and aqueous electrolytes

Synthesis of reduced graphene oxide (rGO) using coconut husk as a green and natural resource for supercapacitor (SC) applications.

Fracture Process Analysis and Deformation-Induced Toughening of Double-Network Gels

Fracture Process Analysis and Deformation-Induced Toughening of Double-Network Gels

Exploration and Evaluation of Pony Fish (Leiognathus sp) Mince as a Source of Surimi and Study its Spectral and Textural Attributes

Background: This is the first study in Indian context where underutilized fish species pony fish (Leiognathus sp.) has been used for the preparation of surimi and surimi gel and its textural and spectral images were analysed. Methods: Textural profile analysis for estimating the hardness, gumminess and chewiness parameters and colour analyser for measuring the difference in whiteness among samples were used. FTIR (Fourier Transform Infrared Spectroscopy) was used to estimate the percentage of proteins folded during heat denaturation process. Result: Textural parameters of CWS (Conventional Washed Surimi) gel showed ideal gel strength of 191.06 g cm, hardness of 46.48 N, gumminess of 30.75 N and chewiness of 28.70 N. Colour analysis of UM (Unwashed Mince), CWS and CWS gel showed whiteness of 38.59, 61.45 and 72.07. FTIR analysis of UM, CWS and CWS gel shows unfolding of protein structures in the wavelength of 1688.07 cm-1, 1665.34 cm-1 and 1653.20 cm-1. This study reveals the potential use of pony fish (Leiognathus sp.) as one of the favorable fish species for surimi and sausage production showing virtuous instrumental quality attributes.

Synergism in sequential inactivation of Cryptosporidium parvum with trypsin and UV irradiation.

Cryptosporidium, a protozoan parasite, in wastewater presents a major public health concern for water safety. However, bactericidal efficiencies of conventional disinfection methods towards Cryptosporidium oocysts are still hampered owing to the presence of their thick outer wall. In this study, we present a novel UV inactivation process where the efficiency has been significantly enhanced by addition of a trypsin pretreatment stage. Notably, inactivation (log-reduction) of oocysts was noted to be 73.75-294.72% higher than that obtained by UV irradiation alone, under identical conditions. Experimental observations and supporting mechanistic analyses suggest that trypsin led to cleavage of the protein layers on the oocyst wall, facilitating penetration of UV radiation into the oocysts leading to degradation of their genomic DNA (gDNA). The dissociative effect of trypsin on the oocyst wall was indicated by the fact that 64.50% of oocysts displayed early apoptosis after trypsinization. Imaging by scanning electron microscopy indicated that this combined treatment led to substantial disruption of the oocyst coat, deforming their shape. This resulted in the release of cellular proteins and gDNA, their concentrations in bulk solution increasing by 1.22-8.60 times. As UV irradiation time was prolonged, gDNA was degraded into smaller fragments with lower molecular masses. Both laddering and diffuse smear patterns in gel analysis indicated significantly detrimental effects on gDNA and viability of oocysts. Overall, this study demonstrated enhancement of UV inactivation of Cryptosporidium oocysts by trypsin and explored the underlying mechanisms for the process.

Effect of the double heating cycle on the thermal gelling properties of vicilin fractions from soy, mung bean, red bean and their mixture with soy glycinin

This study investigated the effect of a double heating cycle (90 °C) on the thermal gelling behavior of fractionated vicilins from soybean (SV), mung bean (MV) and red bean (RV) with and without soy glycinin (SG). Both MV and RV consisted of peptides with relatively low Mw comparing to those of SV. Differential scanning calorimetry (DSC) indicated that MV and RV had a greater thermal stability than those of SV. Based on oscillatory shear rheometry, the first heating could not cause the gelation of MV and RV, but the thermal gel of both vicilins could be formed by the second heating stage. The stiffness of the RV gel was lower than that of MV. Based on texture profile analysis (TPA), the hardness and springiness of gel prepared by MV did not differ from those of SV, whereas RV gel showed high cohesiveness but low hardness and springiness compared to that of SV (p < 0.05). The gumminess of MV and RV gels was lower than that of SV gel (p < 0.05). The differences in TPA parameters between MV and RV were mainly due to different contributions of hydrophobic and electrostatic interactions, which also affected their microstructures. However, their gel characteristics disappeared when SG was mixed with these vicilins. The results indicated that both MV and RV had a potential to regulate the textural properties of soy protein-based gel matrix, and double heating was necessary to form a viscoelastic thermal gel containing vicilin fractions.

Effects of rice bran feruloyl oligosaccharides on gel properties and microstructure of grass carp surimi

Effects of feruloyl oligosaccharides (FOs) from rice bran on the gel properties, microstructure, and sensory properties of grass crap surimi gel were investigated. The results showed that FOs decreased the whiteness of surimi gel, and improved the water-holding capacity and breaking force of surimi gel. According to the texture analysis, the hardness and chewiness of surimi gel significantly increased by adding 0.3% FOs, but had no significant effect on the springiness and cohesiveness. The changes in AFM images indicated that FOs made myofibrillar protein aggregated and uniformly distributed. The SEM micrograph revealed that the 0.3% FOs group had the most compact and ordered network structure. Additionally, sensory characteristics suggested that FOs reduced off-odor from freshwater fish and remained fish delicious taste. This study provides a new prospect for the potential commercial application of FOs as a health gel enhancer in surimi products.

Two-Dye Versus Three-Dye DIGE for Comparative Testis Tissue Proteomic Analysis.

The global analysis of the proteome is an important tool in cell biology. Comparative proteomic evaluations can identify and compare the composition, dynamics, and modifications between different samples. Comparing tissue proteomes under different conditions is crucial for advancing the biomedical field. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a sensitive and robust biochemical method that can compare multiple protein samples over a broad dynamic range on the same analytical gel and can be used to establish differentially expressed protein profiles between different sample groups. 2D-DIGE involves fluorescently labeling protein samples with CyDye flours, via a two-dye or a three-dye system, pre-separation by isoelectric point, and molecular weight. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization, thus enabling accurate high-resolution analysis of differences in protein abundance between samples. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of two-dye and three-dye DIGE minimal labeling.

A Spectroscopic Approach to Unravel the Local Conformations of a G-Quadruplex Using CD-Active Fluorescent Base Analogues.

The formation of a stable G-quadruplex (GQ) can inhibit the increased telomerase activity that is common in most cancers. The global structure and the thermal stability of the GQs are usually evaluated by spectroscopic methods and thermal denaturation properties. However, most biochemical processes involving GQs might require local conformational changes at the guanine tetrad (G4) level. These local conformational changes of individual G4 layers during protein and drug interactions have not yet been explored in detail. In this study, we monitored the local conformations of individual G4 layers in GQs using 6-methylisoxanthopterine (6MI) chromophores, which are circular dichroism (CD)-active fluorescent base analogues of guanine, as local conformational probes. A synthetic, tetramolecular, parallel GQ with site-specifically positioned 6MI monomers or dimers was used as the experimental construct. Analytical ultracentrifugation studies and gel electrophoretic studies showed that properly positioned 6MI monomers and dimers could form stable GQs with CD-active fluorescent G4 layers. The local conformation of individual fluorescent G4 layers in the GQ structure was then tracked by monitoring the absorbance, fluorescence intensity, thermal melting, fluorescence quenching, and CD changes of the incorporated probes. Overall, these studies showed that site-specifically incorporated fluorescent base analogues could be used as probes to monitor the local conformational changes of individual G4 layers of a GQ structure. This method can be applied to explore the details of small molecule-GQ interaction at the level of the individual G4 layers, which may prove to be useful in designing drugs to treat GQ-related genetic disorders, cancer, and aging.

Development and characterization of amphotericin B nanoemulsion-loaded mucoadhesive gel for treatment of vulvovaginal candidiasis

Despite being recognized as the “gold standard” for treating azole-resistant vulvovaginal candidiasis, amphotericin B (AmB), an amphoteric molecule, has not been widely used due to serious issues with solubility and permeability. In light of the aforementioned, the objective of the present study was to increase AmB's therapeutic efficacy by formulating it into an o/w nanoemulsion (AmB-NE) system. Furthermore, to facilitate AmB-NE's retention within the vaginal cavity, it was loaded into a mixture of Carbopol® 974P and Aloe vera-based gel (CA gel). Briefly, in the present study, a kinetically stable batch of formulated AmB-NE having a globule size of 76.52 ± 3.11 nm, PDI of 0.342 ± 0.032, and zeta potential of -22.32 ± 0.88 mV was incorporated into the CA gel base. This AmB-NE loaded gel (AmB-NE gel) exhibited a non-Fickian/anomalous diffusion from the hydrophilic matrix. The texture analysis of AmB-NE gel revealed that the prepared gel was a non-drip, soft, easy to spread, and sufficiently cohesive gel that could reside in the vaginal cavity, which was confirmed by our ex-vivo retention test, which revealed that AmB-NE loaded gel could stay in the vaginal cavity for approximately 11 h. Ex-vivo skin permeation studies revealed that AmB-NE is 4.26 times more permeable than AmB-coarse gel, implying that AmB-NE facilitates AmB entry into the vaginal epithelial layers. Furthermore, in-vivo vaginal lavage studies revealed that AmB-NE gel permeated 7.03-fold more than AmB-coarse gel. Prepared AmB-NE gel was stable in refrigerated condition and showed no histopathological toxicity. Thus, the present study suggests that AmB-NE gel could eliminate the existing problem of AmB and that it could serve as an alternative option to treat vulvovaginal candidiasis.