Search results for: linker histone

Authors: Sridhar A. Malkaram, Tamer E. Fandy

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Purpose: 5-Azacytidine (5AC) and decitabine (DC) are DNA hypomethylating agents. We recently demonstrated that both drugs increase the enzymatic activity of the histone deacetylase enzyme SIRT6. Accordingly, we are comparing the changes H3K9 acetylation changes in the whole genome induced by both drugs using leukemia cells. Description of Methods & Materials: Mononuclear cells from the bone marrow of six de-identified naive acute myeloid leukemia (AML) patients were cultured with either 500 nM of DC or 5AC for 72 h followed by ChIP-Seq analysis using a ChIP-validated acetylated-H3K9 (H3K9ac) antibody. Chip-Seq libraries were prepared from treated and untreated cells using SMARTer ThruPLEX DNA- seq kit (Takara Bio, USA) according to the manufacturer’s instructions. Libraries were purified and size-selected with AMPure XP beads at 1:1 (v/v) ratio. All libraries were pooled prior to sequencing on an Illumina HiSeq 1500. The dual-indexed single-read Rapid Run was performed with 1x120 cycles at 5 pM final concentration of the library pool. Sequence reads with average Phred quality < 20, with length < 35bp, PCR duplicates, and those aligning to blacklisted regions of the genome were filtered out using Trim Galore v0.4.4 and cutadapt v1.18. Reads were aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in end-to-end alignment mode. H3K9ac enriched (peak) regions were identified using diffReps v1.55.4 software using input samples for background correction. The statistical significance of differential peak counts was assessed using a negative binomial test using all individuals as replicates. Data & Results: The data from the six patients showed significant (Padj<0.05) acetylation changes at 925 loci after 5AC treatment versus 182 loci after DC treatment. Both drugs induced H3K9 acetylation changes at different chromosomal regions, including promoters, coding exons, introns, and distal intergenic regions. Ten common genes showed H3K9 acetylation changes by both drugs. Approximately 84% of the genes showed an H3K9 acetylation decrease by 5AC versus 54% only by DC. Figures 1 and 2 show the heatmaps for the top 100 genes and the 99 genes showing H3K9 acetylation decrease after 5AC treatment and DC treatment, respectively. Conclusion: Despite the similarity in hypomethylating activity and chemical structure, the effect of both drugs on H3K9 acetylation change was significantly different. More changes in H3K9 acetylation were observed after 5 AC treatments compared to DC. The impact of these changes on gene expression and the clinical efficacy of these drugs requires further investigation.

Keywords: DNA methylation, leukemia, decitabine, 5-Azacytidine, epigenetics

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Authors: L. Szymanski, Z. Kolacinski, Z. Kamiński, G. Raniszewski, J. Fraczyk, L. Pietrzak

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In the article the development and demonstration of method and the model device for hyperthermic selective destruction of cancer cells are presented. This method was based on the synthesis and functionalization of carbon nanotubes serving as ferromagnetic material nano containers. Methodology of the production carbon - ferromagnetic nanocontainers includes: the synthesis of carbon nanotubes, chemical and physical characterization, increasing the content of ferromagnetic material and biochemical functionalization involving the attachment of the key addresses. Biochemical functionalization of ferromagnetic nanocontainers is necessary in order to increase the binding selectively with receptors presented on the surface of tumour cells. Multi-step modification procedure was finally used to attach folic acid on the surface of ferromagnetic nanocontainers. Folic acid is ligand of folate receptors which is overexpresion in tumor cells. The presence of ligand should ensure the specificity of the interaction between ferromagnetic nanocontainers and tumor cells. The chemical functionalization contains several step: oxidation reaction, transformation of carboxyl groups into more reactive ester or amide groups, incorporation of spacer molecule (linker), attaching folic acid. Activation of carboxylic groups was prepared with triazine coupling reagent (preparation of superactive ester attached on the nanocontainers). The spacer molecules were designed and synthesized. In order to ensure biocompatibillity of linkers they were built from amino acids or peptides. Spacer molecules were synthesized using the SPPS method. Synthesis was performed on 2-Chlorotrityl resin. The linker important feature is its length. Due to that fact synthesis of peptide linkers containing from 2 to 4 -Ala- residues was carried out. Independent synthesis of the conjugate of foilic acid with 6-aminocaproic acid was made. Final step of synthesis was connecting conjugat with spacer molecules and attaching it on the ferromagnetic nanocontainer surface. This article contains also information about special CVD and microvave plasma system to produce nanotubes and ferromagnetic nanocontainers. The first tests in the device for hyperthermal RF generator will be presented. The frequency of RF generator was in the ranges from 10 to 14Mhz and from 265 to 621kHz.

Keywords: synthesis of carbon nanotubes, hyperthermia, ligands, carbon nanotubes

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Authors: Evgeniya Y. Yuzbasheva, Tigran V. Yuzbashev, Natalia I. Perkovskaya, Elizaveta B. Mostova

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Cell-surface display of lipase is of great interest as it has many applications in the field of biotechnology owing to its unique advantages: simplified product purification, and cost-effective downstream processing. One promising area of application for whole-cell biocatalysts with surface displayed lipase is biodiesel synthesis. Biodiesel is biodegradable, renewable, and nontoxic alternative fuel for diesel engines. Although the alkaline catalysis method has been widely used for biodiesel production, it has a number of limitations, such as rigorous feedstock specifications, complicated downstream processes, including removal of inorganic salts from the product, recovery of the salt-containing by-product glycerol, and treatment of alkaline wastewater. Enzymatic synthesis of biodiesel can overcome these drawbacks. In this study, Lip2p lipase was displayed on Yarrowia lipolytica cells via C- and N-terminal fusion variant. The active site of lipase is located near the C-terminus, therefore to prevent the activity loosing the insertion of glycine-serine linker between Lip2p and C-domains was performed. The hydrolytic activity of the displayed lipase reached 12,000–18,000 U/g of dry weight. However, leakage of enzyme from the cell wall was observed. In case of C-terminal fusion variant, the leakage was occurred due to the proteolytic cleavage within the linker peptide. In case of N-terminal fusion variant, the leaking enzyme was presented as three proteins, one of which corresponded to the whole hybrid protein. The calculated number of recombinant enzyme displayed on the cell surface is approximately 6–9 × 105 molecules per cell, which is close to the theoretical maximum (2 × 106 molecules/cell). Thus, we attribute the enzyme leakage to the limited space available on the cell surface. Nevertheless, cell-bound lipase exhibited greater stability to short-term and long-term temperature treatment than the native enzyme. It retained 74% of original activity at 60°C for 5 min of incubation, and 83% of original activity after incubation at 50°C during 5 h. Cell-bound lipase had also higher stability in organic solvents and detergents. The developed whole-cell biocatalyst was used for recycling biodiesel synthesis. Two repeated cycles of methanolysis yielded 84.1–% and 71.0–% methyl esters after 33–h and 45–h reactions, respectively.

Keywords: biodiesel, cell-surface display, lipase, whole-cell biocatalyst

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Authors: A. Shahsavar, Z. Jakub

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Due to the outstanding properties of the 2D metal-organic frameworks (MOF), intensive computational and experimental studies have been done. However, the lack of fundamental studies of MOFs on the graphene backbone is observed. This work studies Fe and Ni as metal and tetracyanoquinodimethane (TCNQ) with a high electron affinity as an organic linker functionalized on graphene. Here we present DFT calculations results to unveil the electronic and magnetic properties of iron and nickel-TCNQ physisorbed on graphene. Adsorption and Fermi energies, structural, and magnetic properties will be reported. Our experimental observations prove Fe- and NiTCNQ@Gr/Ir(111) are thermally highly stable up to 500 and 250°C, respectively, making them promising materials for single-atom catalysts or high-density storage media.

Keywords: DFT, graphene, MTCNQ, self-assembly

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Authors: S. T. Kumbhar, M. S. Bhatia, R. C. Khairate

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An effective nanodrug delivery system was developed by using chitosan for increased encapsulation efficiency and retarded release of curcumin. Potential ionotropic gelation method was used for the development of chitosan nanoparticles with TPP as cross-linker. The characterization was done for analysis of size, structure, surface morphology, and thermal behavior of synthesized chitosan nanoparticles. The encapsulation efficiency was more than 80%, with improved drug loading capacity. The in-vitro drug release study showed that curcumin release rate was decreased significantly. These chitosan nanoparticles could be a suitable platform for co-delivery of curcumin and anticancer agent for enhanced cytotoxic effect on tumor cells.

Keywords: Curcumin, chitosan, nanoparticles, anticancer activity

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Authors: P. Asiabi, M. Shahhoseini, R. Favaedi, F. Hassani, N. Nassiri, B. Movaghar, L. Karimian, P. Eftekhariyazdi

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Introduction: Polycystic Ovary Syndrome is a common gynecologic disorder. Many factors including environment, metabolism, hormones and genetics are involved in etiopathogenesis of PCOS. Of genes that have altered expression in human reproductive system disorders are HOX family genes which act as transcription factors in regulation of cell proliferation, differentiation, adhesion and migration. Since recent evidences consider epigenetic factors as causative mechanisms of PCOS, evaluation of association between known epigenetic marks of acetylation/methylation of histone 3 (H3K9ac/me) with regulatory regions of these genes can represent better insight about PCOS. In the current study, cumulus cells (CCs) which have critical roles during folliculogenesis, oocyte maturation, ovulation and fertilization were aimed to monitor epigenetic alterations of HOX genes. Material and methods: CCs were collected from 20 PCOS patients and 20 fertile women (18-36 year) with male infertility problems referred to the Royan Institute to have ICSI under GnRH antagonist protocol. Informed consents were obtained from the participants. Thirty six hours after hCG injection, ovaries were punctured and cumulus oocyte complexes were dissected. Soluble chromatin were extracted from CCs and Chromatin Immune precipitation (ChIP) coupled with Real Time PCR was performed to quantify the epigenetic marks of histone H3K9 acetylation/methylation (H3K9ac/me) on regulatory regions of 15 members of HOX genes from A-D subfamily. Results: Obtained data showed significant increase of H3K9ac epigenetic mark on regulatory regions of HOXA1, HOXB2, HOXC4, HOXD1, HOXD3 and HOXD4 (P < 0.01) and HOXC5 (P < 0.05) and also significant decrease of H3K9ac into regulatory regions of HOXA2, HOXA4, HOXA5, HOXB1 and HOXB5 (P < 0.01) and HOXB3 (P<0.05) in PCOS patients vs. control group. On the other side, there was a significant decrease in incorporation of H3K9me level on regulatory region of HOXA2, HOXA3, HOXA4, HOXA5, HOXB3 and HOXC4 (P≤0.01) and HOXB5 (P < 0.05) in PCOS patients vs. control group. This epigenetic mark (H3K9me2) has significant increase on regulatory region of HOXB1, HOXB2, HOXC5, HOXD1, HOXD3 and HOXD4 (P ≤ 0.01) and HOXB4 (P < 0.05) in patients vs. control group. There were no significant changes in acetylation/methylation levels of H3K9 on regulatory regions of the other studied genes. Conclusion: Current study suggests that epigenetic alterations of HOX genes can be correlated with PCOS and consequently female infertility. This finding might offer additional definitions of PCOS, and eventually provides insight for novel treatments with epidrugs for this disease.

Keywords: epigenetic, HOX genes, PCOS, female infertility

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Authors: Srinivas Bathini, Duraichelvan Raju, Simona Badilescu, Muthukumaran Packirisamy

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A bio-sensing method, based on the plasmonic property of gold nano-islands, has been developed for detection of exosomes in a clinical setting. The position of the gold plasmon band in the UV-Visible spectrum depends on the size and shape of gold nanoparticles as well as on the surrounding environment. By adsorbing various chemical entities, or binding them, the gold plasmon band will shift toward longer wavelengths and the shift is proportional to the concentration. Exosomes transport cargoes of molecules and genetic materials to proximal and distal cells. Presently, the standard method for their isolation and quantification from body fluids is by ultracentrifugation, not a practical method to be implemented in a clinical setting. Thus, a versatile and cutting-edge platform is required to selectively detect and isolate exosomes for further analysis at clinical level. The new sensing protocol, instead of antibodies, makes use of a specially synthesized polypeptide (Vn96), to capture and quantify the exosomes from different media, by binding the heat shock proteins from exosomes. The protocol has been established and optimized by using a glass substrate, in order to facilitate the next stage, namely the transfer of the protocol to a microfluidic environment. After each step of the protocol, the UV-Vis spectrum was recorded and the position of gold Localized Surface Plasmon Resonance (LSPR) band was measured. The sensing process was modelled, taking into account the characteristics of the nano-island structure, prepared by thermal convection and annealing. The optimal molar ratios of the most important chemical entities, involved in the detection of exosomes were calculated as well. Indeed, it was found that the results of the sensing process depend on the two major steps: the molar ratios of streptavidin to biotin-PEG-Vn96 and, the final step, the capture of exosomes by the biotin-PEG-Vn96 complex. The microfluidic device designed for sensing of exosomes consists of a glass substrate, sealed by a PDMS layer that contains the channel and a collecting chamber. In the device, the solutions of linker, cross-linker, etc., are pumped over the gold nano-islands and an Ocean Optics spectrometer is used to measure the position of the Au plasmon band at each step of the sensing. The experiments have shown that the shift of the Au LSPR band is proportional to the concentration of exosomes and, thereby, exosomes can be accurately quantified. An important advantage of the method is the ability to discriminate between exosomes having different origins.

Keywords: exosomes, gold nano-islands, microfluidics, plasmonic biosensing

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Authors: Vijayakameswara Rao Neralla, Jueun Jeon, Jae Hyung Park

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To develop a potential nanocarrier for diagnosis and treatment of rheumatoid arthritis (RA), we prepared a hyaluronic acid (HA)-5β-cholanic acid (CA) conjugate with an acid-labile ketal linker. This conjugate could self-assemble in aqueous conditions to produce pH-responsive HA-CA nanoparticles as potential carriers of the anti-inflammatory drug methotrexate (MTX). MTX was rapidly released from nanoparticles under inflamed synovial tissue in RA. In vitro cytotoxicity data showed that pH-responsive HA-CA nanoparticles were non-toxic to RAW 264.7 cells. In vivo biodistribution results confirmed that, after their systemic administration, pH-responsive HA-CA nanoparticles selectively accumulated in the inflamed joints of collagen-induced arthritis mice. These results indicate that pH-responsive HA-CA nanoparticles represent a promising candidate as a drug carrier for RA therapy.

Keywords: rheumatoid arthritis, hyaluronic acid, nanocarrier, self-assembly, MTX

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Authors: Areej K. Al-Jwaid, Dmitiry Berllio, Andrew Cundy, Irina Savina, Jonathan L. Caplin

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Phenol is a toxic compound that is widely distributed in the environment including the atmosphere, water and soil, due to the release of effluents from the petrochemical and pharmaceutical industries, coking plants and oil refineries. Moreover, a range of daily products, using phenol as a raw material, may find their way into the environment without prior treatment. The toxicity of phenol effects both human and environment health, and various physio-chemical methods to remediate phenol contamination have been used. While these techniques are effective, their complexity and high cost had led to search for alternative strategies to reduce and eliminate high concentrations of phenolic compounds in the environment. Biological treatments are preferable because they are environmentally friendly and cheaper than physico-chemical approaches. Some microorganisms such as Pseudomonas sp., Rhodococus sp., Acinetobacter sp. and Bacillus sp. have shown a high ability to degrade phenolic compounds to provide a sole source of energy. Immobilisation process utilising various materials have been used to protect and enhance the viability of cells, and to provide structural support for the bacterial cells. The aim of this study is to develop a new approach to the bioremediation of phenol based on an immobilisation strategy that can be used in wastewater. In this study, two bacterial species known to be phenol degrading bacteria (Pseudomonas mendocina and Rhodococus koreensis) were purchased from National Collection of Industrial, Food and Marine Bacteria (NCIMB). The two species and mixture of them were immobilised to produce macro porous crosslinked cell cryogels samples by using four types of cross-linker polymer solutions in a cryogelation process. The samples were used in a batch culture to degrade phenol at an initial concentration of 50mg/L at pH 7.5±0.3 and a temperature of 30°C. The four types of polymer solution - i. glutaraldehyde (GA), ii. Polyvinyl alcohol with glutaraldehyde (PVA+GA), iii. Polyvinyl alcohol–aldehyde (PVA-al) and iv. Polyetheleneimine–aldehyde (PEI-al), were used at different concentrations, ranging from 0.5 to 1.5% to crosslink the cells. The results of SEM and rheology analysis indicated that cell-cryogel samples crosslinked with the four cross-linker polymers formed monolithic macro porous cryogels. The samples were evaluated for their ability to degrade phenol. Macro porous cell–cryogels crosslinked with GA and PVA+GA showed an ability to degrade phenol for only one week, while the other samples crosslinked with a combination of PVA-al + PEI-al at two different concentrations have shown higher stability and viability to reuse to degrade phenol at concentration (50 mg/L) for five weeks. The initial results of using crosslinked cell cryogel samples to degrade phenol indicate that is a promising tool for bioremediation strategies especially to eliminate and remove the high concentration of phenol in wastewater.

Keywords: bioremediation, crosslinked cells, immobilisation, phenol degradation

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Authors: Rajesh A. Rane, Shital S. Naphade, Rajshekhar Karpoormath

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Thiozolidin-4-one, a mimic of thiazolobenzimidazole (TBZ) has drawn many attentions due to its potent and selective inhibition against the HIV-1 and low toxicity by binding to the allosteric site of the reverse transcriptase (RT) as a non-nucleoside RT inhibitor (NNRTI). Similarly, marine bromopyrrole alkaloids are well known for their diverse array of anti-infective properties. Hence, we have reported synthesis and in vitro HIV-1 RT inhibitory activity of a series of 4-thiazolidinone-bromopyrrole alkaloid hybrids tethered with amide linker. The results of in vitro HIV-1 RT kit assay showed that some of the compounds, such as 4c, 4d, and 4i could effectively inhibit RT activity. Among them, compounds 4c having 4-chlorophenyl substituted 4-thiazolidione ring was the best one with the IC50 value of 0.26 µM. The sturdy emerges with key structure-activity relationship that pyrrole-NH-free core benefited inhibition against HIV-1 RT inhibition. This study identified conjugate 4c with potent activity and selectivity as promising compound for further drug development to HIV.

Keywords: antiviral drugs, bromopyrrole alkaloids, HIV-1 RT inhibition, 4-thiazolidinone

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Authors: Chang-Hui Shen, Michelle Esposito, Andrew J. Shen, Michael Adejokun, Diana Laterman

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The packaging of DNA into nucleosomes is critical to genomic compaction, yet it can leave gene promoters inaccessible to activator proteins or transcription machinery and thus prevents transcriptional initiation. Both chromatin remodelers and histone acetylases (HATs) are the two main transcription co-activators that can reconfigure chromatin structure for transcriptional activation. Ino80p is the core component of the INO80 remodeling complex. Recently, it was shown that Ino80p dissociates from the yeast INO1 promoter after induction. However, when certain HATs were deleted or mutated, Ino80p accumulated at the promoters during gene activation. This suggests a link between HATs’ presence and Ino80p’s dissociation. However, it has yet to be demonstrated that Ino80p can be acetylated. To determine if Ino80p can be acetylated, wild-type Saccharomyces cerevisiae cells carrying Ino80p engineered with a double FLAG tag (MATa INO80-FLAG his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) were grown to mid log phase, as were non-tagged wild type (WT) (MATa his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) and ino80∆ (MATa ino80∆::TRP1 his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) cells as controls. Cells were harvested, and the cell lysates were subjected to immunoprecipitation (IP) with α-FLAG resin to isolate Ino80p. These eluted IP samples were subjected to SDS-PAGE and Western blot analysis. Subsequently, the blots were probed with the α-FLAG and α-acetyl lysine antibodies, respectively. For the blot probed with α-FLAG, one prominent band was shown in the INO80-FLAG cells, but no band was detected in the IP samples from the WT and ino80∆ cells. For the blot probed with the α-acetyl lysine antibody, we detected acetylated Ino80p in the INO80-FLAG strain while no bands were observed in the control strains. As such, our results showed that Ino80p can be acetylated. This acetylation can explain the co-activator’s recruitment patterns observed in current gene activation models. In yeast INO1, it has been shown that Ino80p is recruited to the promoter during repression, and then dissociates from the promoter once de-repression begins. Histone acetylases, on the other hand, have the opposite pattern of recruitment, as they have an increased presence at the promoter as INO1 de-repression commences. This Ino80p recruitment pattern significantly changes when HAT mutant strains are studied. It was observed that instead of dissociating, Ino80p accumulates at the promoter in the absence of functional HATs, such as Gcn5p or Esa1p, under de-repressing processes. As such, Ino80p acetylation may be required for its proper dissociation from the promoters. The remodelers’ dissociation mechanism may also have a wide range of implications with respect to transcriptional initiation, elongation, or even repression as it allows for increased spatial access to the promoter for the various transcription factors and regulators that need to bind in that region. Our findings here suggest a previously uncharacterized interaction between Ino80p and other co-activators recruited to promoters. As such, further analysis of Ino80p acetylation not only will provide insight into the role of epigenetic modifications in transcriptional activation, but also gives insight into the interactions occurring between co-activators at gene promoters during gene regulation.

Keywords: acetylation, chromatin remodeler, epigenetic modification, Ino80p

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Authors: Nagasamy Venkatesh Dhandapani

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This work aims at investigating the use of β-Cyclodextrin as a cross linker, in an attempt to formulate nanosponges containing ketoconazole. The nanosponges were prepared by cross-linking method. The excipients used in this study did not alter the physicochemical properties of a drug as revealed by FTIR spectroscopy. Studies on various formulation variables revealed that all the variables are inter-related with the formulation. The ideal batch among the formulation was selected based on the higher entrapment efficiency and drug loading. The in vitro release studies of ketoconazole nanosponges in hydrogel exhibited a sustained release over a period of 24 hours. Mathematical analysis of drug release from the formulation followed non-Fickian diffusion obeying first order kinetics. The anti-fungal activity of the formulation exhibited better zone of inhibition when compared to pure drug (ketoconazole) against Tinea corporis.

Keywords: nanosponges, beta-cyclodextrin, ketoconazole, tinea corporis

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Authors: Sasan Talebnezhad, Saeed Pormahdian, Naghi Assali

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Homogeneous α-diimine nickel (II) catalyst complexes, with and without amino para-aryl position functionality, were synthesized. These complexes were immobilized on carboxyl, hydroxyl, and acyl chloride functionalized multi-walled carbon nanotubes to form five novel heterogeneous α-diiminonickel catalysts. Immobilization was performed by covalent or electrostatic bonding via methylaluminoxane (MAO) linker or amide linkage. Both the nature of α-diimine ligands and the kind of interaction between anchored catalyst complexes and multi-walled carbon nanotube surface influenced the catalytic performance, microstructure, and morphology of obtained polyethylenes. The catalyst prepared by amide bonding showed lowest relative weight loss in thermogravimetry analysis and highest activities up to 5863 gr PE mmol-1Ni.hr-1. This catalyst produced polyethylene with dense botryoidal morphology.

Keywords: α-diimine nickel (II) complexes, immobilization, multi-walled carbon nanotubes, ethylene polymerization

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Authors: Sasan Talebnezhad, Saeed Pourmahdian, Naghi Assali

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Homogeneous α-diimine nickel (II) catalyst complexes, with and without amino para-aryl position functionality, were synthesized. These complexes were immobilized on carboxyl, hydroxyl and acyl chloride functionalized multi-walled carbon nanotubes to form five novel heterogeneous α diiminonickel catalysts. Immobilization was performed by covalent or electrostatic bonding via methylaluminoxane (MAO) linker or amide linkage. Both the nature of α-diimine ligands and the kind of interaction between anchored catalyst complexes and multi-walled carbon nanotube surface influenced the catalytic performance, microstructure, and morphology of obtained polyethylenes. The catalyst prepared by amide bonding showed lowest relative weight loss in thermogravimetry analysis and highest activities up to 5863 gr PE mmol-1Ni.hr-1. This catalyst produced polyethylene with dense botryoidal morphology.

Keywords: α-diimine nickel (II) complexes, immobilization, multi-walled carbon nanotubes, ethylene polymerization

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Authors: Sujosh Nandi, Proshanta Guha

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Synthetic plastics are preferred for food packaging due to high strength, stretch-ability, good water vapor and gas barrier properties, transparency and low cost. However, environmental pollution generated by these synthetic plastics is a major concern of modern human civilization. Therefore, use of biodegradable polymers as a substitute for synthetic non-biodegradable polymers are encouraged to be used even after considering drawbacks related to mechanical and barrier properties of the films. Starch is considered one of the potential raw material for the biodegradable polymer, encounters poor water barrier property and mechanical properties due to its hydrophilic nature. That apart, recrystallization of starch molecules occurs during aging which decreases flexibility and increases elastic modulus of the film. The recrystallization process can be minimized by blending of other hydrocolloids having similar structural compatibility, into the starch matrix. Therefore, incorporation of guar gum having a similar structural backbone, into the starch matrix can introduce a potential film into the realm of biodegradable polymer. However, hydrophilic nature of both starch and guar gum, water barrier property of the film is low. One of the prospective solution to enhance this could be modification of the potato starch/guar gum (PSGG) composite film using cross-linker. Over the years, several cross-linking agents such as phosphorus oxychloride, sodium trimetaphosphate, etc. have been used to improve water vapor permeability (WVP) of the films. However, these chemical cross-linking agents are toxic, expensive and take longer time to degrade. Therefore, naturally available carboxylic acid (tartaric acid, malonic acid, succinic acid, etc.) had been used as a cross-linker and found that water barrier property enhanced substantially. As per our knowledge, no works have been reported with tartaric acid and succinic acid as a cross-linking agent blended with the PSGG films. Therefore, the objective of the present study was to examine the changes in water vapor barrier property and mechanical properties of the PSGG films after cross-linked with tartaric acid (TA) and succinic acid (SA). The cross-linkers were blended with PSGG film-forming solution at four different concentrations (4, 8, 12 & 16%) and cast on teflon plate at 37°C for 20 h. From the fourier-transform infrared spectroscopy (FTIR) study of the developed films, a band at 1720cm-1 was observed which is attributed to the formation of ester group in the developed films. On the other hand, it was observed that tensile strength (TS) of the cross-linked film decreased compared to non-cross linked films, whereas strain at break increased by several folds. Moreover, the results depicted that tensile strength diminished with increasing the concentration of TA or SA and lowest TS (1.62 MPa) was observed for 16% SA. That apart, maximum strain at break was also observed for TA at 16% and the reason behind this could be a lesser degree of crystallinity of the TA cross-linked films compared to SA. However, water vapor permeability of succinic acid cross-linked film was reduced significantly, but it was enhanced significantly by addition of tartaric acid.

Keywords: cross linking agent, guar gum, organic acids, potato starch

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Authors: Frank Boris Feutmba Keutchou, Saurelle Fabienne Bieghan Same, Verelle Elsa Fogang Pokam, Charles Ursula Metapi Meikeu, Angel Marilyne Messop Nzomo, Ousman Tamgue

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Infectious diseases are one of the most important causes of morbidity and mortality worldwide. These diseases are caused by micro-pathogenic organisms, such as bacteria, viruses, parasites, and fungi. Heritable changes in gene expression that do not involve changes to the underlying DNA sequence are referred to as epigenetics. Emerging evidence suggests that epigenetic mechanisms are important in the emergence and progression of infectious diseases. Pathogens can manipulate host epigenetic machinery to promote their own replication and evade immune responses. The Human Genome Project has provided new opportunities for developing better tools for the diagnosis and identification of target genes. Several epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNA expression, have been shown to influence infectious disease outcomes. Understanding the epigenetic mechanisms underlying infectious diseases may result in the progression of new therapeutic approaches focusing on host-pathogen interactions. The goal of this study is to show how different infectious agents interact with host cells after infection.

Keywords: epigenetic, infectious disease, micro-pathogenic organism, phenotype

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Authors: Raied, Badr Al-Fulaiti, E. I. El-Shafey

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Cyclodextrin (CD) derivatives (αCD, βCD, ϒCD and hp-βCD) were successfully immobilized on silica gel surface via epichlorohydrin as a cross linker. The ratio of silica to CD was optimized in preliminary experiments based on best performance of iodine adsorption capacity. Selected adsorbents with ratios of silica to CD derivatives, in this study, include Si-αCD (3:2), Si-βCD (4:1), Si-ϒCD (4:1) and Si-hp-βCD (4:1). The adsorption of iodine (I2/KI) solution was investigated in terms of initial pH, contact time, iodine concentration and temperature. No significant variations was noticed for iodine adsorption at different pH values, thus, initial pH 6 was selected for further studies. Equilibrium adsorption was reached faster on Si-hp-βCD than other adsorbents with kinetic adsorption data fitting well pseudo second order model. Activation energy (Ea) was found to be in the range of 12.7 - 23.4 kJ/mol. Equilibrium adsorption data were found to fit well the Langmuir adsorption model with lower uptake as temperature rises. Iodine uptake follows the order: Si-hp-βCD (714 mg/g) >Si-αCD (625 mg/g) >Si-βCD (555.6 mg/g)> Si-ϒCD (435 mg/g). Thermodynamic study showed that iodine adsorption is exothermic and spontaneous. Adsorbents reuse exhibited excellent performance for iodine adsorption with a decrease in iodine uptake of ~ 2- 4 % in the third adsorption cycle.

Keywords: adsorption, iodine, silica, cyclodextrin, functionalization, epichlorohydrin

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

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Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

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Authors: Abul B. M. M. K. Islam, Nuria Lopez-Bigas, Elizaveta V. Benevolenskaya

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RBP2 has shown to be important for cell differentiation control through epigenetic mechanism. The main aim of the present study is genome-wide location analysis of human RBP2 isoforms that differ in a histone-binding domain by ChIPseq. It is conceivable that the larger isoform (LI) of RBP2, which contains a specific H3K4me3 interacting domain, differs from the smaller isoform (SI) in genomic location, may account for the observed diversity in RBP2 function. To distinguish the two RBP2 isoforms, we used the fact that the SI lacks the C-terminal PHD domain and hence used the antibodies detecting both RBP2 isoforms (AI) through a common central domain, and the antibodies detecting only LI but not SI, through a C-terminal PHD domain. Overall our analysis suggests that RBP2 occupies about 77 nucleotides and binds GC rich motifs of active genes, does not bind to centromere, telomere, or enhancer regions, and binding sites are conserved compare to random. A striking difference between the only-SI and only-LI is that a large number of only-SI peaks are located in CpG islands and close to TSS compared to only-LI peaks. Enrichment analysis of the related genes indicates that several oncogenic pathways and metabolic pathways/processes are significantly enriched among only-SI/AI targets, but not LI/only-LI peak’s targets.

Keywords: bioinformatics, cancer, ChIP-seq, KDM5A

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Authors: Yasmina Houda Bendahma, Tewfik Bouchaour, Meriem Merad, Ulrich Maschke

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The purpose of this work is to study retention of dye dissolved in distilled water, by an hydrophilic acrylic polymer network. The polymer network considered is Poly (2-hydroxyethyl methacrylate) (PHEMA): it is prepared by photo-polymerization under UV irradiation in the presence of a monomer (HEMA), initiator and an agent cross-linker. PHEMA polymer network obtained can be used in the retention of dye molecules present in the wastewater. The results obtained are interesting in the study of the kinetics of swelling and de-swelling of cross linked polymer networks PHEMA in colored aqueous solutions. The dyes used for retention by the PHEMA networks are eosin Y and Malachite Green, dissolved in distilled water. Theoretical conformational study by a simplified molecular model of system cross linked PHEMA / dye (eosin Y and Malachite Green), is used to simulate the retention phenomenon (or Docking) dye molecules in cavities in nano-domains included in the PHEMA polymer network.

Keywords: dye retention, molecular modeling, photochemically crosslinked polymer network, swelling deswelling, PHEMA, HEMA

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Authors: Mingxi Zhou, Jiří Kubásek, Iva Mozgová

Abstract:

In Arabidopsis thaliana, histone 3 lysine 27 tri-methylation catalysed byPRC2 is playing essential functions in the regulation of plant development, growth, and reproduction[1-2]. Despite numerous studies related to the role of PRC2 in developmental control, how PRC2 works in the operational control in plants is unknown. In the present, the evidence that PRC2 probably participates in the regulation of retrograde singalling pathway in Arabidopsisis found. Firstly, we observed that the rosette size and biomass in PRC2-depletion mutants (clf-29 and swn-3) is significantly higher than WTunder medium light condition (ML: 125 µmol m⁻² s⁻²), while under medium high light condition (MHL: 300 µmol m⁻² s-2), the increase was reverse. Under ML condition, the photosynthesis related parameters determined by fluorCam did not show significant differences between WT and mutants, while the pigments concentration increased in the leaf of PRC2-depletion mutants, especially in swn. The dynamic of light-responsive genes and circadian clock genes expression by RT-qPCRwithin 24 hours in the mutants were comparable to WT. However, we observed upregulation of photosynthesis-associated nuclear genes in the PRC2-depletion mutants under chloroplast damaging condition (treated by lincomycin), corresponding to the so-called genome uncoupled (gun) phenotype. Here, we will present our results describing these phenotypes and our suggestion and outlook for studying the involvement of PRC2 in chloroplast-to-nucleus retrograde signalling.

Keywords: PRC2, retrograde signalling, light acclimation, photosyntheis

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Authors: Majede Modheji, Hamid Emadi, Hossein Vojoudi

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An efficient magnetic mesoporous structure was designed and prepared for the facile pre-concentration of As(III) ions. To prepare the sorbent, a core-shell magnetic silica nanoparticle was covered by MCM-41 like structure, and then the surface was modified by guanidine via an amine linker. The prepared adsorbent was investigated as an effective and sensitive material for the adsorption of arsenic ions from the aqueous solution applying a normal batch method. The imperative variables of the adsorption were studied to increase efficiency. The dynamic and static processes were tested that matched a pseudo-second order of kinetic model and the Langmuir isotherm model, respectively. The sorbent reusability was investigated, and it was confirmed that the designed product could be applied at best for six cycles successively without any significant efficiency loss. The synthesized product was tested to determine and pre-concentrate trace amounts of arsenic ions in rice and natural waters as a real sample. A desorption process applying 5 mL of hydrochloric acid (0.5 mol L⁻¹) as an eluent exhibited about 98% recovery of the As(III) ions adsorbed on the GA-MSMP sorbent.

Keywords: arsenic, adsorption, mesoporous, surface modification, MCM-41

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Authors: Aniket Kumar, Jacob Peedicayil

Abstract:

Major depressive disorder (MDD) is a common and important psychiatric disorder. Several clinical features of MDD suggest an epigenetic basis for its pathogenesis. Since epigenetics (heritable changes in gene expression not involving changes in DNA sequence) may underlie the pathogenesis of MDD, epigenetic drugs such as DNA methyltransferase inhibitors (DNMTi) and histone deactylase inhibitors (HDACi) may be useful for treating MDD. The available literature indexed in Pubmed on preclinical drug trials of epigenetic drugs for the treatment of MDD was investigated. The search terms we used were ‘depression’ or ‘depressive’ and ‘HDACi’ or ‘DNMTi’. Among epigenetic drugs, it was found that there were 3 preclinical trials using HDACi and 3 using DNMTi for the treatment of MDD. All the trials were conducted on rodents (mice or rats). The animal models of depression that were used were: learned helplessness-induced animal model, forced swim test, open field test, and the tail suspension test. One study used a genetic rat model of depression (the Flinders Sensitive Line). The HDACi that were tested were: sodium butyrate, compound 60 (Cpd-60), and valproic acid. The DNMTi that were tested were: 5-azacytidine and decitabine. Among the three preclinical trials using HDACi, all showed an antidepressant effect in animal models of depression. Among the 3 preclinical trials using DNMTi also, all showed an antidepressant effect in animal models of depression. Thus, epigenetic drugs, namely, HDACi and DNMTi, may prove to be useful in the treatment of MDD and merit further investigation for the treatment of this disorder.

Keywords: DNA methylation, drug discovery, epigenetics, major depressive disorder

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Authors: Mir Hussain Nawaz, Lyudmila Nedyalkova, Haizhong Zhu, Wael M. Rabeh

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In this study, we aim to biochemically and structurally characterize the interactions of human HK2 with the mitochondria in addition to the role of its N-terminal domain in catalysis and stability of the full-length enzyme. Here, we solved the crystal structure of human HK2 in complex with glucose and glucose-6-phosphate (PDB code: 2NZT), where it is a homodimer with catalytically active N- and C-terminal domains linked by a seven-turn α-helix. Different from the inactive N-terminal domains of isozymes 1 and 3, the N- domain of HK2 not only capable to catalyze a reaction but it is responsible for the thermodynamic stabilizes of the full-length enzyme. Deletion of first α-helix of the N-domain that binds to the mitochondria altered the stability and catalytic activity of the full-length HK2. In addition, we found the linker helix between the N- and C-terminal domains to play an important role in controlling the catalytic activity of the N-terminal domain. HK2 is a major step in the regulation of glucose metabolism in cancer making it an ideal target for the development of new anticancer therapeutics. Characterizing the structural and molecular mechanisms of human HK2 and its role in cancer metabolism will accelerate the design and development of new cancer therapeutics that are safe and cancer specific.

Keywords: cancer metabolism, enzymology, drug discovery, protein stability

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Authors: Lawrence Mzukisi Madikizela, Luke Chimuka

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Removal of organics from wastewater offers a better water quality, therefore, the purpose of this work was to investigate the use of molecularly imprinted polymer (MIP) for the elimination of selected organics from water. A multi-template MIP for the adsorption of naproxen, ibuprofen and diclofenac was synthesized using a bulk polymerization method. A MIP was synthesized at 70°C by employing 2-vinylpyridine, ethylene glycol dimethacrylate, toluene and 1,1’-azobis-(cyclohexanecarbonitrile) as functional monomer, cross-linker, porogen and initiator, respectively. Thermogravimetric characterization indicated that the polymer backbone collapses at 250°C and scanning electron microscopy revealed the porous and roughness nature of the MIP after elution of templates. The performance of the MIP in aqueous solutions was evaluated by optimizing several adsorption parameters. The optimized adsorption conditions were 50 mg of MIP, extraction time of 10 min, a sample pH of 4.6 and the initial concentration of 30 mg/L. The imprinting factors obtained for naproxen, ibuprofen and diclofenac were 1.25, 1.42, and 2.01, respectively. The order of selectivity for the MIP was; diclofenac > ibuprofen > naproxen. MIP showed great swelling in water with an initial swelling rate of 2.62 g/(g min). The synthesized MIP proved to be able to adsorb naproxen, ibuprofen and diclofenac from contaminated deionized water, wastewater influent and effluent.

Keywords: adsorption, molecularly imprinted polymer, multi template, pharmaceuticals

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Authors: Ramalingam Boobalan, Chinpiao Chen, Jui-I. Chiao

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A series of erlotinib analogues that have structural modification at 6,7-alkoxyl positions is efficiently synthesized. The key reactions that involved in synthesis are one-pot oxime formation-dehydration for the formation of nitrile, quinazoline ring formation reaction between aniline and o-cyanoaniline via formamidine intermediate, Fe/NH4Cl catalyzed reduction-hetereocyclization-reductive ring opening reaction for the formation of o-aminobenzamide, high yielding seal tube reactions for O-demethylation, sodium iodide substitution, ammonia substitution. The in vitro anti-tumor activity of synthesized compounds is studied in two non-small cell lung cancer (NSCLC) cell lines (A549 and H1975). Among the synthesized compounds, the iodo compound 6 (ETN-6) exhibits higher anti-cancer activity compared to erlotinib. An efficient method is developed for the conjugation of erlotinib analogue-4, alcohol compound, with protein, bovine serum albumin (BSA), via succinic acid linker. The in vitro anti-tumor activity of the protein attached erlotinib analogue, 8 (ETN-4-Suc-BSA), showed stronger inhibitory activity in both A549 and H1975 NSCLC cell lines.

Keywords: anti-cancer, BSA, EGFR, Erlotinib

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Authors: Vishal Kumar Gupta

Abstract:

Purpose: This study has been undertaken to develop novel pH sensitive interpenetrating network hydrogel beads. Methods: The pH sensitive PAAM-g-Guar gum copolymer was synthesized by free radical polymerization followed by alkaline hydrolysis. Beads of guar gum-grafted-polyacrylamide and sodium Carboxy methyl cellulose (Na CMC) loaded with Pantoprazole sodium were prepared and evaluated for pH sensitivity, swelling properties, drug entrapment efficiency and in vitro drug release characteristics. Seven formulations were prepared for the drug with varying polymer and cross linker concentrations. Results: The grafting and alkaline hydrolysis reactions were confirmed by FT-IR spectroscopy. Differential scanning calorimetry was carried out to know the compatibility of encapsulated drug with the polymers. Scanning electron microscopic study revealed that the IPN beads were spherical. The entrapment efficiency was found to be in the range of 85-92%. Particle size analysis was carried out by optical microscopy. As the pH of the medium was changed from 1.2 to 7.4, a considerable increase in swelling was observed for all beads. Increase in the copolymer concentration showed sustained the drug release up to 12 hrs. Drug release from the beads followed super case II transport mechanism. Conclusion: It was concluded that guar gum-acrylamide beads, cross-linked with aluminum chloride offer an opportunity for controlled drug release of pantoprazole sodium.

Keywords: IPN, hydrogels, DSC, SEM

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Authors: Riddhi Trivedi, Shrenik Shah

Abstract:

For Si RNA to be delivered various biodegradable polymers are trialed by many researchers. One of them is Chitosan (CS) nanoparticles which have been extensively studied for siRNA delivery but the stability and efficacy of such particles are highly dependent on the types of cross-linker used. Hence the attempts are made in this study with PGA To address this issue, three common cross-linkers; Ethylene glycol diacrylate (ED) and poly-D-glutamic acid (PGA) were used to prepare siRNA loaded CS-ED/PGA nanoparticles by ionic gelation method. The nanoparticles which were obtained were compared for its characterization in terms of its physicochemical properties i.e. particle size of the resultant particles, zeta potential, its encapsulation capacity in the polymer. Among all the formulations prepared with different crosslinker PGA siRNA had the smallest particle size (ranged from 120 ± 1.7 to 500 ± 10.9 nm) with zeta potential ranged from 22.1 ± 1.5 to +32.4 ± 0.5 mV, and high entrapment ( > 91%) and binding efficiencies. Similarly, CS-ED nanoparticles showed better siRNA protection during storage at 4˚C and as determined by serum protection assay. TEM micrographs revealed the assorted morphology of CS-PGA-siRNA nanoparticles in contrast to irregular morphology displayed by CS-ED-siRNA. All siRNA loaded nanoparticles were found to give initial burst release which after some time followed by a sustained release of siRNA which were loaded inside. All the formulations showed concentration-dependent cytotoxicity with when cytotoxicity performed by HeLa and normal vero cell lines.

Keywords: chitosan, siRNA, cytotoxicity, cell line study

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Authors: Michal Natan, Ori Gutman, Shlomo Margel, Ehud Banin

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Biofilm formation is a serious problem in medical and industrial settings due to the increased resistance of these communities to killing compared to free-living bacteria. This has prompted the search for agents that can inhibit both bacterial growth and biofilm formation. In this study, N-halamine rechargeable nanoparticles (NPs) were synthesized by co-polymerization of the monomer methacryl amide and the cross-linker monomer N,N-methylene bisacryl amide, and were subsequently loaded with Cl+, using bleach. The chlorinated NPs exhibited remarkable stability to organic reagents. The antibacterial mechanism of the P(MAA-MBAA)-Cl NPs involved generation of reactive oxygen species (ROS) only upon exposure to organic media, but not upon incubation in water, suggesting a specific activation. Moreover, a unique interaction of the P(MAA-MBAA)-Cl NPs with Staphylococcus aureus bacteria but not with human cells was discovered, whereby these microorganisms were all specifically targeted and marked for destruction. Finally, in collaboration with Netafim Ltd. irrigation drippers containing the P(MAA-MBAA)-Cl were incubated in the field and were shown to prevent fouling on them for 5 months as opposed to the control drippers that exhibited substantial fouling. Further, the NPs offer recharging to the surface, thus providing long-lasting protection that does not exist in the products available today. Taken together, the results demonstrate the great potential of implementing the charged NPs in devices and surfaces to prevent bacterial growth.

Keywords: bacteria, biofilm, fouling, nanoparticles

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Authors: Mazita Mohd Diah, Anton V. Dolzhenko, Tin Wui Wong

Abstract:

Nanoparticles, being small with a large specific surface area, increase solubility, enhance bioavailability, improve controlled release and enable precision targeting of the entrapped compounds. In this study, chitosan as polymeric permeation enhancer was conjugated to a polar pro-drug, carboxymethyl-5-fluorouracil (CMFU) to increase the skin drug permeation. Chitosan-CMFU conjugate was synthesized using chemical conjugation process through succinate linker. It was then transformed into nanoparticles via spray drying method. The conjugation was elucidated using Fourier Transform Infrared and Proton Nuclear Magnetic Resonance techniques. The nanoparticle size, size distribution, zeta potential, drug content, skin permeation and retention profiles were characterized. The conjugation was denoted using 1H NMR by new peaks at signal δ = 4.184 ppm (singlet, 2H for CH2) and 7.676-7.688 ppm (doublet, 1H for C6) attributed to CMFU in chitosan-CMFU NMR spectrum. The nanoparticles had profiles of particle size: 93.97 ±35.11 nm, polydispersity index: 0.40 ± 0.14, zeta potential: +18.25 ±2.95 mV and drug content: 6.20 ± 1.98 % w/w. Almost 80 % w/w CMFU in the form of nanoparticles permeated through the skin in 24 hours and close to 50 % w/w permeation occurred in first 1-2 hours. Without conjugation to chitosan and nanoparticulation, less than 40 % w/w CMFU permeated through the skin in 24 hours. The skin drug retention likewise was higher with chitosan-CMFU nanoparticles (15.34 ± 5.82 % w/w) than CMFU (2.24 ± 0.57 % w/w). CMFU, through conjugation with chitosan permeation enhancer and processed in nanogeometry, had its skin permeation and retention degree promoted.

Keywords: carboxymethyl-5-fluorouracil, chitosan, conjugate, skin permeation, skin retention

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