Dye Binding Research Articles

Formation of amyloid fibrils by the regulatory 14-3-3ζ protein.

The 14-3-3 proteins are a highly conserved adaptor protein family with multi-layer functions, abundantly expressed in the brain. The 14-3-3 proteins modulate phosphorylation, regulate enzymatic activity and can act as chaperones. Most importantly, they play an important role in various neurodegenerative disorders due to their vast interaction partners. Particularly, the 14-3-3ζ isoform is known to co-localize in aggregation tangles in both Alzheimer's and Parkinson's diseases as a result of protein-protein interactions. These abnormal clumps consist of amyloid fibrils, insoluble aggregates, mainly formed by the amyloid-β, tau and α-synuclein proteins. However, the molecular basis of if and how 14-3-3ζ can aggregate into amyloid fibrils is unknown. In this study, we describe the formation of amyloid fibrils by 14-3-3ζ using a comprehensive approach that combines bioinformatic tools, amyloid-specific dye binding, secondary structure analysis and atomic force microscopy. The results presented herein characterize the amyloidogenic properties of 14-3-3ζ and imply that the well-folded protein undergoes aggregation to β-sheet-rich amyloid fibrils.

A Near-Real-Time Ficin-Based Enzyme Assay for Biomonitoring of Heavy Metals Pollution in Waters Near the Langkawi UNESCO Kilim Karst Geoforest Park

Near-real-time biomonitoring, especially when utilizing enzyme assays, offers exceptional sensitivity to bioavailable pollutants, yielding swift results favorable to immediate action. This approach is particularly crucial in the context of mitigating pollution in drinking water systems, safeguarding both human and animal health. This study presents an application of a previously developed enzyme assay in biomonitoring to detect pollutants, specifically heavy metals, in environmental samples from the UNESCO’s Kilim Karst Geoforest Park. Utilizing the ficin dye binding assay, developed for mercury (Hg2+), silver (Ag+), and copper (Cu2+) detection at the sub ppm level, we demonstrated its effectiveness in identifying low concentrations of these metals in marine and brackish waters. The assay provided a sensitive, rapid, and cost-effective monitoring, showing negligible inhibition (<10%) over a 6-hour field trial, indicating low pollution levels and verified using instrumental analysis. This approach enables the early detection of environmental contaminants, facilitating timely interventions and contributing to the protection of ecotourism sites by providing evidence-based data for policymaking. The simplicity and visual appeal of the enzyme assays also make them excellent educational tools, promoting environmental awareness and conservation efforts. Our findings underscore the potential of enzyme assays for widespread environmental assessment, aligning local monitoring practices with international standards and fostering global collaboration in environmental protection. This study not only contributes to our understanding of ecological health in marine and brackish waters but also highlights the importance of continuous monitoring to preserve natural habitats.

A Near-Real-Time Achromopeptidase-Based Enzyme Assay for Biomonitoring of Zinc Pollution in Kuah's Jetty in Langkawi

Enzyme-based assay in near-real-time biomonitoring provides high sensitivity to bioavailable contaminants, leading to quick results that support prompt action. It is essential to use this method to reduce pollution in drinking, agriculture and marine waters and protect the health of both humans and animals. This work applies a previously discovered enzyme test in biomonitoring to identify contaminants, particularly zinc, in marine water samples from the Langkawi Island, an island that harbors the UNESCO's Geoforest Park status. We used the achromopeptidase dye binding assay, specifically designed for detecting mercury zinc at levels below one part per million, to identify trace amounts of these metal successfully. The test demonstrated a sensitive, quick, and cost-efficient monitoring method with little inhibition (<10%) during a 6-hour field trial for three consecutive days, suggesting low pollution levels and confirmed by instrumental analysis. This method allows for the prompt identification of environmental pollutants, which helps take appropriate actions and safeguard ecotourism locations by offering data-driven information for policy development. Enzyme tests are simple and visually appealing, making them effective instructional tools that help raise environmental awareness and support conservation initiatives. Our research highlights the need to use enzyme tests for broad environmental evaluation, harmonizing local monitoring methods with global standards, and promoting international cooperation in environmental conservation. This work enhances our comprehension of ecological well-being in marine and brackish waterways and underscores the significance of ongoing monitoring to protect natural environments.

Molecular recognition of synthetic RNAs by phenothiazinium dyes methylene blue and new methylene blue: Thermodynamic approach

Many biological process and function centers around recognition of double stranded RNA as it impacts numerous pathways associated with maturation of cellular RNA. This work assembles an intricate thermodynamic profiling of the phenothaizinium dyes methylene blue and new methylene blue with three double stranded ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) with aid of thermal helix melting, isothermal titration calorimetry and differential scanning calorimetry experiments. Isothermal titration calorimetry had put forward that highest binding affinity was observed for poly(A).poly(U)-dye binding while the order varied as poly(A).poly(U) > poly(C).poly(G) > poly(I).poly(C). Strong stability of the polynucleotides against heat strand separation characterises the binding. Non-electrostatic component had larger share in parsing of the standard molar Gibbs energy of the binding. The processes' negative change in heat capacity is evidence of how essential hydrophobic forces are. Release of water molecules which are in random orientation mode occurs from RNA's hydrophobic binding pockets. Negative enthalpy and positive entropic change are the two significant features in this hydrophobic binding scenario. Another vital result of enthalpy-entropy compensation has been identified with the binding processes. The findings bear direct and ubiquitous acknowledgement in revitalizing our interest and broadening our horizon towards successful targeting of small molecules to RNAs.

The MA Helix Is Important for Receptor Assembly and Function in the α4β2 nACh Receptor.

Pentameric ligand-gated ion channels (pLGICs) are expressed throughout the central and peripheral nervous systems of vertebrates and modulate many aspects of human health and disease. Recent structural and computational data indicate that cation-selective pLGICs contain a long helical extension (MA) of one of the transmembrane helices. The MA helix has been shown to affect both the membrane expression of, and ion conductance levels through, these pLGICs. Here we probe the functional effects of 68 mutations in the MA region of the α4β2 nicotinic acetylcholine receptor (nAChR), using a voltage-sensitive membrane dye and radioligand binding to measure receptor function and expression/assembly. We found seven alanine mutations in a stretch of the MA helix that prevent correct receptor folding and/or assembly, as evidenced by the lack of both function and ligand binding. A further two alanine mutations resulted in receptors that were capable of binding ligand but showed no functional response, and we propose that, in these mutants, ligand binding is insufficient to trigger channel opening. The data clarify the effect of the MA helix, and as the effects of some of our mutations in the α4β2 nAChR differ from the effects of equivalent mutations in other cation-selective pLGICs, we suggest that residues in the MA helix may play subtly different roles in different receptors.

Tetracationic bis-triarylborane tetraynes as dual fluorescence and SERS sensors for DNA, RNA and proteins

We report herein two new dual luminescent and Raman (SERS)-active probes, able to sense submicromolar concentrations of DNA and protein in aqueous samples. Both analogues, characterized by a tetrayne linker connecting two triarylborane fluorophores, show high binding affinities and strong fluorescent and SERS responses to ds-DNA, ds-RNA, and protein (BSA). Detailed studies revealed that both the neutral and tetracationic analogue bind to ds-DNA/RNA grooves and protein (BSA) with similar affinities, at variance to previous non-charged triarylboranes, which interacted only with BSA. The fluorimetric response upon binding to BSA was different to that observed for previous analogues; the tetracationic analogue emission was enhanced and the neutral analogue emission quenched, this selectivity being attributed to the difference in solvatochromism of the triarylborane fluorophore (charged vs neutral). The neutral dye did not show any SERS signal due to the lack of interaction with negatively charged Ag nanoparticles, stressing the importance of positive charge for the application of SERS sensing. The SERS signal of the tetrayne linker of the tetracationic analogue was shifted by −81 cm−1 compared to that of the previously studied diyne analogue. The SERS signal intensity change was proportional to dye binding to ds-DNA, and completely quenched by nanomolar concentrations of BSA, such a specific response being attributed to the complete immersion of the dye within BSA.

Small Molecules N-Phenylbenzofuran-2-carboxamide and N-Phenylbenzo[b]thiophene-2-carboxamide Promote Beta-Amyloid (Aβ42) Aggregation and Mitigate Neurotoxicity.

This study reports the unusual ability of small molecules N-phenylbenzofuran-2-carboxamide (7a) and N-phenylbenzo[b]thiophene-2-carboxamide (7b) to promote and accelerate Aβ42 aggregation. In the in vitro aggregation kinetic assays, 7a was able to demonstrate rapid increases in Aβ42 fibrillogenesis ranging from 1.5- to 4.7-fold when tested at 1, 5, 10, and 25 μM compared to Aβ42-alone control. Similarly, compound 7b also exhibited 2.9- to 4.3-fold increases in Aβ42 fibrillogenesis at the concentration range tested. Electron microscopy studies at 1, 5, 10, and 25 μM also demonstrate the ability of compounds 7a and 7b to promote and accelerate Aβ42 aggregation with the formation of long, elongated fibril structures. Both 7a and 7b were not toxic to HT22 hippocampal neuronal cells and strikingly were able to prevent Aβ42-induced cytotoxicity in HT22 hippocampal neuronal cells (cell viability ∼74%) compared to the Aβ42-treated group (cell viability ∼20%). Fluorescence imaging studies using BioTracker 490 green, Hoeschst 33342, and the amyloid binding dye ProteoStat further demonstrate the ability of 7a and 7b to promote Aβ42 fibrillogenesis and prevent Aβ42-induced cytotoxicity to HT22 hippocampal neuronal cells. Computational modeling studies suggest that both 7a and 7b can interact with the Aβ42 oligomer and pentamers and have the potential to modulate the self-assembly pathways. The 8-anilino-1-naphthalenesulfonic acid (ANS) dye binding assay also demonstrates the ability of 7a and 7b to expose the hydrophobic surface of Aβ42 to the solvent surface that promotes self-assembly and rapid fibrillogenesis. These studies demonstrate the unique ability of small molecules 7a and 7b to alter the self-assembly and misfolding pathways of Aβ42 by promoting the formation of nontoxic aggregates. These findings have direct implications in the discovery and development of novel small-molecule-based chemical and pharmacological tools to study the Aβ42 aggregation mechanisms, and in the design of novel antiamyloid therapies to treat Alzheimer's disease.

Capture-SELEX of DNA Aptamers for Sulforhodamine B and Fluorescein.

While many dye binding aptamers have been reported, most of them were for light-up aptamers that can significantly enhance the quantum yield of fluorophores. Sulforhodamine B (SRhB) was used as a target previously to select both DNA and RNA aptamers, and the DNA aptamer was a G-quadruplex that can bind to a number of rhodamine analogs. In addition, the previous selections were performed by immobilizing the target molecules. In this work, the library immobilization method was used to respectively select aptamers for SRhB and fluorescein. The SRhB aptamer has a non-G-quadruplex structure with a Kd of 1.0 μM measured from isothermal titration calorimetry. Upon titration of the aptamer, the fluorescence of SRhB increased 2.5-fold, and this aptamer does not require Mg2+ for binding. Rhodamine B has even tighter binding suggesting binding through the xanthene moiety of the dyes. No binding was detected for fluorescein. For the fluorescein selection, a dominant aptamer sequence with a Kd of 147 μM was obtained. This study provides two new aptamers for two important fluorophores that can be used to study aptamer-based separation, dye detection and catalysis. Comparison of these aptamers also provides insights into the effect of functional groups on aptamer binding.

Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling.

Methylene blue has multiple antiviral properties against Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2). The ability of methylene blue to inhibit different stages of the virus life cycle, both in light-independent and photodynamic processes, is used in clinical practice. At the same time, the molecular aspects of the interactions of methylene blue with molecular components of coronaviruses are not fully understood. Here, we use Brownian dynamics to identify methylene blue binding sites on the SARS-CoV-2 envelope. The local lipid and protein composition of the coronavirus envelope plays a crucial role in the binding of this cationic dye. Viral structures targeted by methylene blue include the S and E proteins and negatively charged lipids. We compare the obtained results with known experimental data on the antiviral effects of methylene blue to elucidate the molecular basis of its activity against coronaviruses.

Cibacron Blue F3GA ligand dye-based magnetic silica particles for the albumin purification.

Dye-ligand affinity chromatography is among the increasingly popular affinity chromatography based on molecular recognition for the purification of albumin. This study focuses on the binding of Cibacron Blue F3GA ligand dye with magnetic silica particles and purification by separation. Mono-disperse silica particles with bimodal pore size distribution were employed as a high-performance adsorbent for human serum albumin (HSA) protein purification under equilibrium conditions. The synthesized ligand-dye affinity based magnetic silica particles were characterized by electron spin resonance, Fourier-transform infrared spectroscopy, scanning electron microscopy, vibrating sample magnetometer, elemental analysis, and dispersive X-ray analysis. The HSA purification performance of the proposed material in the presence of a magnetic field was relatively investigated using magnetic-based particles with similar morphologies. The maximum adsorption capacity for HSA in an artificial plasma medium was defined as 48.6 mg/g magnetic silica particle. By using the designed magnetic silica particles, 1.0 M NaCl solution was successfully utilized for obtaining quantitative desorption with HSA. However, continued HSA purification performances of magnetic-based particles were significantly lower concerning the ligand-dye magnetic silica particles. The purity of the removed albumin was about 97%. The magnetic silica particles could be utilized many times without decreasing their protein adsorption capacities remarkably.

Enterobacter hormaechei Z8b-60: A Tannin Degrading Bacteria Isolated from Slaughterhouse Waste

Tannases or Tannin acyl hydrolases (EC 3.1.1.20) are a family of esterases that catalyze the hydrolysis of ester and depside bonds present in hydrolyzable tannins to release gallic acid. Industrial applications of tannase in food, brewing, chemical, pharmaceutical, and bioremediation, have made it one of the most important enzymes in research. The aim of the present study focused on the degradation of tannic acid by novel bacterial tannase isolated from slaughterhouse waste-enriched soil. Soil containing ruminant microflora is cultured on MSM containing tannic acid. Among four bacterial isolates, a potent strain was cultivated for identification which are then analysed for biochemical characterization and physiological characterization. Bacteria use tannic acid as the sole carbon source for growth and showed maximum growth at 0.6%. The morphology of the isolate shows that it contains gram-negative rods that are nonmotile and capsulated. Based on 16S rRNA and phylogenetic analysis, the isolate was confirmed as Enterobacter hormaechei Z8b-60. Tannase production from bacteria was confirmed by a novel, sensitive plate assay by observing the zone of clearance around colonies and also by dye binding method using methyl gallate as substrate. During the study, TLC and HPLC were performed to analyze the accumulated gallic acid and other metabolites. Intracellular tannase production amplified from 14.98 U/mL to 102.7 U/mL as tannic acid concentration increases from 0.4% to 1.0%, respectively.

Investigation of the Photocatalytic Activity of Electrospun and Surface-Modified PAN/α-FeOOH Nanofibers for the Degradation of Hazardous Azo Dyes.

Decoration of α-FeOOH nanorods over PAN nanofibers was performed using the electrospinning technique. The as-designed decorated nanofibers were characterized using various techniques such as wide-angle powder X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), high-resolution transmission electron microscopy (HRTEM), Fourier transform infrared (FTIR) spectroscopy, UV-vis spectrophotometry (UV-vis), thermogravimetry analysis (TGA), N2 adsorption-desorption isotherm (BET), and X-ray photoelectron spectrometry (XPS). α-FeOOH NRs were decorated uniformly over PAN fibers, as observed from its morphological investigation, which shows novelty. 1D α-FeOOH nanorods with PAN nanofibers have not been studied for photocatalytic characteristics. No literature mentions that α-FeOOH nanorods coated in PAN NFs act as photocatalysts to degrade hazardous azo dyes. α-FeOOH nanorods on PAN NFs inhibit aggregation and increase dye binding, boosting photocatalytic performance. PAN/α-FeOOH NFs have a maximal specific surface area with a reduced bandgap than α-FeOOH NRs. PAN/α-FeOOH nanofibers showed excellent photocatalytic activity for the degradation of Trypan blue (TB) (120 min, 99.7%) and Eriochrome black T (EBT) dyes (160 min, 97.6%), respectively, under solar light irradiation. PAN/α-FeOOH NFs have the potential to be used in the degradation of azo dyes and the treatment of wastewater due to their low energy requirements and versatility.

Clay-Polymer Nanocomposites Mediated Inhibition of Protein Aggregation: Possible Role in the Prevention of Proteinopathies.

The transformation of proteins from their native conformation into highly ordered fibrillar structures due to their misfolding and aggregation under particular conditions are described as beta-sheet enriched amyloid fibrils. The accumulation of these fibrils in different body parts is the major cause of several neurological and non-neurological conditions (proteinopathies). To prevent these proteinopathies, inhibition of protein aggregation is considered a promising strategy. Therefore, in this study, we synthesized montmorillonite (MMT) based poly- orthophenylenediamine (PoPD) nanocomposites (NCs) and characterized their size and morphology due to their remarkable biological properties. Further, the effect of these nanocomposites on inhibition of fibril formation was assessed. These nanocomposites were evaluated for their anti-amyloidogenic potential on two model proteins of amyloidopathies, i.e., human lysozyme and human serum albumin (HL & HSA), by using several biophysical methods, such as Thioflavin T (ThT) and 1-anilino-8-naphthalene sulfonate (ANS) fluorescence, congo red dye binding assay (CR). Secondary structural content was evaluated by Circular dichroism (CD) spectroscopy. Results demonstrated that synthesized nanocomposites significantly inhibited fibril formation in dose-dependent manner that corresponds to their ability to arrest fibrillation. It is suggested that they may adsorb proteins to protect them against aggregation when they are subjected to aggregating conditions. This study offers an opportunity to understand the mechanism of inhibition of fibril formation by nanocomposites, showing that they inhibit amyloid formation and amyloid diseases. Thus, the study concludes that these nanocomposites are promising candidates as therapeutic molecules for proteinopathies and are envisaged to enrich the area of personalized medicine, augmenting the human healthcare system.

Evidence of enhanced inhibitory potential of Ferulic Acid Ethyl Ester towards modulating fibrillation and disassembling insulin fibrils

The conversion of native conformation of protein into proteotoxic insoluble entities is not only confined to the protein misfolding diseases(PMDs) but also associated with pharmaceutically important proteins like insulin during the process of manufacturing/administration. Also all the neurodegenerative diseases are marked with increased level of oxidative stress. Thus finding anti-aggregation agents having anti-oxidant potential is utmost important to combat these complications. Herein, we performed biophysical, computational and imaging techniques to decipher the anti-aggregation propensity of a naturally occurring hydroxycinnamate- Ferulic acid ethyl ester(FAEE) that can cross blood brain barrier. Rayleigh light scattering(RLS) measurements, dye binding assays, Circular dichroism(CD) and Dynamic light scattering(DLS) measurements confirmed the efficient inhibition of insulin fibrillation by FAEE. The Stern-Volmer plot analysis reflected both the static and dynamic quenching mechanism of insulin by FAEE. Molecular docking and simulations results showed that FAEE bind and stabilizes the monomeric state of insulin with binding energy −6.3 kcal/mol. Moreover, the inhibiting effect of FAEE on the elongation phase of onward fibrillation in addition with triggering its fibril disassembling capability was also investigated. Both the stabilization of the protein structure and the restriction of monomers recruitment necessary for the fibrillar growth acts synergistically in providing FAEE its anti-aggregation effect. Appearance of significantly lesser and shortened fibrils in FAEE presence was depicted by transmission electron microscopy. Overall, our finding establishes for the first time the anti-amyloidogenic role of lipophilic FAEE which can cross blood brain barrier. These findings may inspire the development of FAEE based formulations that could possibly treat amyloid-related diseases.

Micro array patch assisted transdermal delivery of high dose, ibuprofen sodium using thermoresponsive sodium alginate/poly (vinylcaprolactam) in situ gels depot

Current study reports the combined technique of microneedle array patches and thermoresponsive gels. Microneedles array patch mediated insitu skin depots were evaluated for sustain drug delivery using sodium alginate/Poly (vinylcaprolactam) thermoresponsive gels. Their phase transition property from sol-gel state was monitored with AR2000 rheometer. Ibuprofen sodium was loaded in optimized formulations. The non-soluble cross-linked microneedle array patches (MAPs) were prepared from variable biocompatible polymers using silicone micromoulds. The fabricated MAPs were evaluated for mechanical stability, inskin dissolution, insertion forces and moisture contents. The penetration depth of MAPs in neonatal rabbit skin was tracked by optical coherence tomography. The optimized MAPs (GP10000) were used as microporation source in skin owing to their stable nature. Pores formation in skin samples after MAPs treatment was confirmed by optical coherence tomography, dye binding and skin integrity analysis. The invitro permeation of Ibuprofen sodium from formulations was studied using Franz cells across intact skin and MAPs applied skin. It was concluded from the results that Ibuprofen sodium permeation was observed for longer time through MAPs treated skin as compared to intact skin. Confocal study confirmed the diffusion of drug loaded formulations in deeper tissues with higher intensity.

Assessing cationic dye adsorption mechanisms on MIL-53 (Al) nanostructured MOF materials using quantum chemical and molecular simulations: Toward environmentally sustainable wastewater treatment

The escalating levels of environmental pollutants, particularly cationic dyes, present a significant ecological threat. Cationic dyes such as rhodamine B (RB) and methylene blue (MB) are extensively used in diverse industrial applications and are known to exert detrimental effects on the environment. The focus of this study revolves around comprehensively examining the adsorption mechanisms associated with the binding of cationic dyes, namely, RB and MB, onto pristine and carboxylic acid (CXA)-modified MIL-53 (Al) nanostructures. By employing quantum mechanics and molecular simulations, this research elucidates the molecular-level behavior of materials and dyes during the adsorption process. The findings demonstrate that incorporating CXA groups enhances MIL-53 (Al)'s adsorption capacity for both RB and MB dyes. Furthermore, the simulations unveil that RB and MB dye adsorption onto the unmodified and modified MIL-53 (Al) materials occurs primarily through electrostatic, van der waals interactions, π-π stacking, and hydrogen bonding. Notably, RB dye exhibits superior reactivity and stability compared to MB dye, owing to its higher adsorption energy. This study provides valuable insights into cationic dye adsorption on nanostructured MIL-53 (Al), emphasizing the suitability of CXA-modified MIL-53 (Al) nanostructures for cationic dye removal from contaminated wastewater. The outcomes of this investigation hold the potential for developing cutting-edge technologies exhibiting superior efficiency and effectiveness for removing cationic dyes, thereby contributing to environmental preservation and public health. Ultimately, this study highlights the prospects of leveraging quantum mechanics and molecular simulations to anticipate the behavior of nanostructured materials and optimize their properties for wastewater treatment.

Molecular characterization of multidrug-resistant avian pathogenic Escherichia coli isolated from poultry and poultry products

Overall occurrence of Escherichia coli in the current study was 7.55% and corresponding group wise occurrence was 13%, 2.66%, 10% and 7% in a faecal and cloacal samples, environmental samples, Retailer’s shop’s samples, and restaurant samples respectively. Amongst the different type of samples processed, highest recovery was from samples collected at poultry farms (13%) followed by Retailer’s shop (10%) suggesting heavy infection and contamination occurring at the initial points of poultry chain. In this study, four isolates failed to exhibit pathogenic potential of E. coli by using in - vitro pathogenic assays viz. Congo red dye binding assay and haemolysis by using 5% sheep blood agar, also turned out to be negative on virulent marker based PCR, suggesting proficient efficacy of targeted genes viz. ecp and uidA for precise and time saving determination of pathogenic potential of E. coli isolates. Besides, one isolate recovered from raw chicken meat sample showed resistance against all 15 antibiotics and other two isolates recovered from litter samples showed resistance against 14 antibiotics suggesting development of multi-drug resistance in common food pathogens, against the most widely used and effective drug of choices in animal as well as human medicine.

KED gene expression in early response to wounding stress in tomato plants.

The wounding-responsive KED gene, named for its coding for a lysine (K), glutamic acid (E), and aspartic acid (D)-rich protein, is widely present among land plants. However, little is known about its regulation or function. In this study, we found that transcription of the tomato (Solanum lycopersicum) KED gene, SlKED, was rapidly and transiently elevated by wounding or ethephon treatment. Compared to the wild-type plants, the CRISPR/Cas9-mediated SlKED knockout plants did not exhibit altered expression patterns for genes involved in hormone biosynthesis or stress signaling, suggesting a lack of pleiotropic effect on other stress-responsive genes. Conversely, jasmonic acid did not appear to directly regulate SlKED expression. Wounded leaves of the KED-lacking plants exhibited higher binding of Evans blue dye than the wild-type, indicating a possible role for KED in healing damaged tissues. The SlKED knockout plants showed a similar dietary effect as the wild-type on the larval growth of tobacco hornworm. But a higher frequency of larval mandible (mouth) movement was recorded during the first 2 minutes of feeding on the wounded KED-lacking SlKED knockout plants than on the wounded KED-producing wild-type plants, probably reflecting an initial differential response by the feeding larvae to the SlKED knockout plants. Our findings suggest that SlKED may be an ethylene-mediated early responder to mechanical stress in tomato, acting downstream of the wound stress response pathways. Although its possible involvement in response to other biotic and abiotic stresses is still unclear, we propose that SlKED may play a role in plant's rapid, short-term, early wounding responses, such as in cellular damage healing.

Activating the delivery of a model drug to lipid membrane by encapsulation of cyclodextrin: Combined experimental and molecular docking studies

Drug delivery science is always an important topic as it studies the delivery of therapeutic payloads to the desired target cells without affecting the healthy tissues/cells, thus minimizing drug-induced toxicity. Aiming towards the targeted drug delivery, the present project deals with the delivery of a polarity-sensitive solvatochromic model drug, namely, salt of 8-anilinonaphthalene-1-sulphonic acid (ANSA) to the model bio-membrane (which mimic several aspects of the real cell membrane), more precisely at the lipid-water interface of L–α-Dipalmitoylphosphatidylcholine (DPPC) phospholipid. The drug delivery process has been activated through the binding of dye with cyclodextrin, acting as a drug transporter. Detailed steady-state and time-resolved spectroscopic studies including molecular docking analysis imply the targeted drug delivery of dye, ANSA, towards the lipid-water interface region of lipid bilayers through encapsulation within the cyclodextrin void. Stronger binding interaction of the dye with the lipid bilayers relative to β-cyclodextrin (β-CD) is the foremost reason for the targeted delivery. The present biophysical interaction studies of drug-lipid interaction, thus, may provide a cordial approach for drug formulation and drug delivery.

Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis.

A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native-PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS-PAGE gels or the edge of the flat SDS-MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen-antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5-6h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.