Slight vapor deficit accelerates graft union healing of tomato plug seedling

The application of grafting in tomato production has substantially improved tomato quality and yields. It has been demonstrated that humidity plays an important role in the graft healing of seedlings. This study focuses on the optimum relative humidity (RH) conditions for scion and rootstock healing of grafted tomato (Solanum lycopersicum L.) seedlings. Two tomato cultivars, ‘Super Sunload’ and ‘Super Dotaerang’, grafted onto ‘B-Blocking’ rootstock were subjected to one of three RH regimens: 70–80, 80–90, or 90–100%. The results showed that the scions of both cultivars showed apparent wilting under the 70–80 and 80–90% RH treatments. On this basis, the 90–100% RH treatment was subdivided into 95–96, 97–98, and 99–100% RH treatments, which were then applied. Among these subdivided RH treatments, the fresh weights of the scions and rootstocks significantly increased in response to the treatments of 97–98 and 99–100% RH, and the graft union connection of both cultivars was also enhanced after two days of healing. Furthermore, lower levels of endogenous H₂O₂ and less activity of antioxidant enzymes were observed in both cultivars in response to treatment with 95–96 or 97–98% RH, which indicated that less oxidative stress occurred. Overall, it is suggested that 97–98% is the optimal RH level for the graft healing of tomato seedlings.     

Phenol, 2,4-bis(1,1-dimethylethyl) of marine bacterial origin inhibits quorum sensing mediated biofilm formation in the uropathogen Serratia marcescens

Intercellular communication in bacteria (quorum sensing, QS) is an important phenomenon in disease dissemination and pathogenesis, which controls biofilm formation also. This study reports the anti-QS and anti-biofilm efficacy of seaweed Gracilaria gracilis associated Vibrio alginolyticus G16 against Serratia marcescens. Purification and mass spectrometric analysis revealed the active principle as phenol, 2,4-bis(1,1-dimethylethyl) [PD]. PD affected the QS regulated virulence factor production in S. marcescens and resulted in a significant (p < 0.05) reduction in biofilm (85%), protease (41.9%), haemolysin (69.9%), lipase (84.3%), prodigiosin (84.5%) and extracellular polysaccharide (84.62%) secretion without hampering growth, as evidenced by XTT [2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] assay. qPCR analysis confirmed the down-regulation of the fimA, fimC, flhD and bsmA genes involved in biofilm formation. Apart from biofilm inhibition and disruption, PD increased the susceptibility of S. marcescens to gentamicin when administered synergistically, which opens another avenue for combinatorial therapy where PD can be used to enhance the efficacy of conventional antibiotics.     

Antiproliferative and Apoptotic Effects of pH-Responsive Veratric Acid-Loaded Polydopamine Nanoparticles in Human Triple Negative Breast Cancer Cells

Veratric acid (VA) is plant-derived phenolic acid known for its therapeutic potential, but its anticancer effect on highly invasive triple-negative breast cancer (TNBC) is yet to be evaluated. Polydopamine nanoparticles (nPDAs) were chosen as the drug carrier to overcome VA's hydrophobic nature and ensure a sustained release of VA. We prepared pH-sensitive nano-formulations of VA-loaded nPDAs and subjected them to physicochemical characterization and in vitro drug release studies, followed by cell viability and apoptotic assays on TNBC cells (MDA-MB-231 cells). The SEM and zeta analysis revealed spherical nPDAs were uniform size distribution and good colloidal stability. In vitro drug release from VA-nPDAs was sustained, prolonged and pH-sensitive, which could benefit tumor cell targeting. MTT and cell viability assays showed that VA-nPDAs (IC50=17.6 μM) are more antiproliferative towards MDA-MB-231 cells than free VA (IC50=437.89 μM). The induction of early and late apoptosis by VA-nPDAs in the cancer cells was identified using annexin V and dead cell assay. Thus, the pH response and sustained release of VA from nPDAs showed the potential to enter the cell, inhibit cell proliferation, and induce apoptosis in human breast cancer cells, indicating the anticancer potential of VA.     

FROG - Fingerprinting Genomic Variation Ontology

Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.     

Biodegradable collagen from Scomberomorus lineolatus skin for wound healing dressings and its application on antibiofilm properties

The major resolution of the study was to develop a dynamic form of natural biopolymer material to improve the wound healing by inhibition of biofilm formation on the surface. The extraction of collagen was effectively prepared from Scomberomorus lineolatus fish skin. Lyophilized collagen sheet was liquefied in 0.5M acetic acid to form acidic solubilized collagen (ASC) for further analysis. Physicochemical characterization of ASC was performed by various techniques using a standard protocol. The yield of ASC form S.lineolatus is higher (21.5%) than the previous reported studies. The effect of collagen solubility is gradually decreases with increasing concentration of NaCl and collagen is mostly soluble in acidic pH conditions. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of ASC contains α chain composition of α₁ and α₂ subunits and was characterized as type I collagen. Ultraviolet absorption was regulated as the appropriate wavelength to optimize the collagen. Fourier-transform infrared spectroscopy and X-ray diffraction confirmed that the isolated collagen is a triple-helical structure. The biofilm formation of Pseudomonas aeruginosa was significantly reduced by collagen incorporated with isolated 3,5,7-trihydroxyflavone (collagen-TF) sheet up to 70%. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide assay executed on fibroblast cell lines (L929) shows that the collagen-TF sheet was 100% compatible to enrich the cell adhesion and proliferation. The current study was the first report to extract, purify, and characterize ASC from S. lineolatus fish skin and characterize as type I collagen. Based on the result, we design the natural biodegradable collagen loaded with TF compound (collagen-TF) for antibiofilm properties. Compared with different sources of polymer, fish skin collagen is more effective and can be used as a biopolymer sheet for wound healing, food, drug delivery, tissue engineering, and pharmaceutical application.     

Membrane elastic fluctuations and the insertion and tilt of beta-barrel proteins

Folding of porin-like beta-barrel outer membrane proteins can be achieved in the presence of phospholipid vesicles, and takes place concurrently with incorporation into the membrane. The pronounced dependence found for the insertion of the protein OmpA on membrane thickness (Kleinschmidt, J. H., and L. K. Tamm. 2002. J. Mol. Biol. 324:319-330) is analyzed in terms of the effects of out-of-plane elastic fluctuations on the area dilation modulus (Evans, E., and W. Rawicz. 1990. Phys. Rev. Lett. 64:2094-2097). For unstrained large unilamellar vesicles, the elastic free energy for membrane insertion is predicted to depend on the fourth power of the membrane thickness. The influence of thermally induced bending fluctuations on the effective tilt of the OmpA beta-barrel in disaturated phosphatidylcholine membranes of different thicknesses (Ramakrishnan, M., J. Qu, C. L. Pocanschi, J. H. Kleinschmidt, and D. Marsh. 2005. Biochemistry. 44:3515-3523) is also considered. A contribution to the orientational order parameter that scales as the inverse second power of the membrane thickness is predicted.     

Correct folding of the beta-barrel of the human membrane protein VDAC requires a lipid bilayer

Spontaneous membrane insertion and folding of beta-barrel membrane proteins from an unfolded state into lipid bilayers has been shown previously only for few outer membrane proteins of Gram-negative bacteria. Here we investigated membrane insertion and folding of a human membrane protein, the isoform 1 of the voltage-dependent anion-selective channel (hVDAC1) of mitochondrial outer membranes. Two classes of transmembrane proteins with either alpha-helical or beta-barrel membrane domains are known from the solved high-resolution structures. VDAC forms a transmembrane beta-barrel with an additional N-terminal alpha-helix. We demonstrate that similar to bacterial OmpA, urea-unfolded hVDAC1 spontaneously inserts and folds into lipid bilayers upon denaturant dilution in the absence of folding assistants or energy sources like ATP. Recordings of the voltage-dependence of the single channel conductance confirmed folding of hVDAC1 to its active form. hVDAC1 developed first beta-sheet secondary structure in aqueous solution, while the alpha-helical structure was formed in the presence of lipid or detergent. In stark contrast to bacterial beta-barrel membrane proteins, hVDAC1 formed different structures in detergent micelles and phospholipid bilayers, with higher content of beta-sheet and lower content of alpha-helix when inserted and folded into lipid bilayers. Experiments with mixtures of lipid and detergent indicated that the content of beta-sheet secondary structure in hVDAC1 decreased at increased detergent content. Unlike bacterial beta-barrel membrane proteins, hVDAC1 was not stable even in mild detergents such as LDAO or dodecylmaltoside. Spontaneous folding of outer membrane proteins into lipid bilayers indicates that in cells, the main purpose of membrane-inserted or associated assembly factors may be to select and target beta-barrel membrane proteins towards the outer membrane instead of actively assembling them under consumption of energy as described for the translocons of cytoplasmic membranes.