Search results for: molecular descriptor

Authors: Taoufik Bettaieb, Sihem Soufi

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As a bioactive metalloid, silicon (Si) is an essential element for plant growth and development. It also plays a crucial role in enhancing plants’ resilience to different abiotic and biotic stresses. The morpho-physiological, biochemical, and molecular background of Si-mediated stress tolerance in plants were unraveled. Cold stress is a severe abiotic stress response to the decrease of plant growth and yield by affecting various physiological activities in plants. Several approaches have been used to alleviate the adverse effects generated from cold stress exposure, but the cost-effective, environmentally friendly, and defensible approach is the supply of silicon. Silicon has the ability to neutralize the harmful impacts of cold stress. Therefore, based on these hypotheses, this study was designed in order to investigate the morphological and physiological background of silicon effects applied at different concentrations on cold stress mitigation during early growth of a turfgrass, namely Paspalum vaginatum Sw. Results show that silicon applied at different concentrations improved the morphological development of Paspalum subjected to cold stress. It is also effective on the photosynthetic apparatus by maintaining stability the photochemical efficiency. As the primary component of cellular membranes, lipids play a critical function in maintaining the structural integrity of plant cells. Silicon application decreased membrane lipid peroxidation and kept on membrane frontline barrier relatively stable under cold stress.

Keywords: crops, cold stress, silicon, abiotic stress

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Authors: Karakhalis N. B.

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This study aimed to determine the prevalence of heparin resistance among cardiac surgical pediatric and neonatal patients and identify associated risk factors. Materials and Methods: The study included 306 pediatric and neonatal patients undergoing on-pump cardiac surgery. Patients whose activated clotting time (ACT) targets were achieved after the first administration of heparin formed the 1st group (n=280); the 2nd group (n=26) included patients with heparin resistance. The initial assessment of the haemostasiological profile included determining the PT, aPPT, FG, AT III activity, and INR. Intraoperative control of heparinization was carried out with a definition of ACT using a kaolin activator. A weight-associated protocol at the rate of 300 U/kg with target values of ACT >480 sec was used for intraoperative heparinization. Results: The heparin resistance was verified in 8.5% of patients included in the study. Repeated heparin administration at the maximum dose of≥600 U/kg is required in 80.77% of cases. Despite additional heparinization, 19.23% of patients had FFP infusion. There was reduced antithrombin activity in the heparin resistance group (p=0.01). Most patients with heparin resistance (57.7%) were pretreated with low molecular weight heparins during the preoperative period. Conclusion: Determining the initial level of antithrombin activity can predict the risk of developing heparin resistance. The factor analysis verified hidden risk factors for heparin resistance to the heparin pretreatment, chronic hypoxia, and chronic heart failure.

Keywords: congenital heart disease, heparin, antithrombin, activated clotting time, heparin resistance

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Authors: Ashfaque Hossain Khan, Brian Thomson, Ratan Debnath, Abhishek Motayed, Mulpuri V. Rao

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Though the efforts had been made, the problem of cross-sensitivity for a single metal oxide-based sensor can’t be fully eliminated. In this work, a sensor array has been designed and fabricated comprising of platinum (Pt), copper (Cu), and silver (Ag) decorated TiO2 and ZnO functionalized GaN nanowires using industry-standard top-down fabrication approach. The metal/metal-oxide combinations within the array have been determined from prior molecular simulation study using first principle calculations based on density functional theory (DFT). The gas responses were obtained for both single and mixture of NO2, SO2, ethanol, and H2 in the presence of H2O and O2 gases under UV light at room temperature. Each gas leaves a unique response footprint across the array sensors by which precise discrimination of cross-sensitive gases has been achieved. An unsupervised principal component analysis (PCA) technique has been implemented on the array response. Results indicate that each gas forms a distinct cluster in the score plot for all the target gases and their mixtures, indicating a clear separation among them. In addition, the developed array device consumes very low power because of ultra-violet (UV) assisted sensing as compared to commercially available metal-oxide sensors. The nanowire sensor array, in combination with PCA, is a potential approach for precise real-time gas monitoring applications.

Keywords: cross-sensitivity, gas sensor, principle component analysis (PCA), sensor array

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Authors: Hye Kyung Kim, Myung-Gyou Kim, Kang-Hyun Leem

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It has been reported that deer antler extract has bone-strengthening activity and effectively used in bone diseases therapy. However, little is known about the cellular and molecular mechanism of this effect. The upper section, mid section, and base of the antler has been known to exhibit different biological properties. Present study investigated the effects of these three parts of deer antler extracts on bone formation and resorption. The effects of deer antler extracts (DH) on bone formation were determined by cell proliferation, alkaline phosphatase (ALP) activity, collagen synthesis, and mineralization in human osteoblastic MG-63 cells. The effect on bone resorption was determined by osteoclastogenesis from bone marrow-derived precursor cells driven by RANKL. Ethanol extracts of DH (50 ~ 100 µg/ml) dose-dependently increased cell proliferation, and upper part increased the cell proliferation by 118.4% while mid and base parts increased proliferation by 107.8% and 102.3%, respectively. ALP activity was significantly increased by upper part of the DH treatment. After enhancement of ALP activity, significant augmentation of collagen synthesis and calcification assessed by Sirus red and Alzarin red staining, respectively, was observed in upper part of the DH treatment. The effect of DH on bone resorption was not observed in all three parts of the DH. These results could provide a mechanistic explanation for the bone-strengthening effects of DH.

Keywords: alkaline phosphatase, collagen synthesis, deer antler, osteoblastic MG-63 cells

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Authors: Adewole Tomiwa Adetunji, Francis Bayo Lewu, Richard Mundembe

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Plants require nitrogen (N) to support desired production levels. There is a need for better understanding of N transport mechanism in order to improve N assimilation by plant root. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which N is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was amplified, sequenced and characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design 976 base pairs AMT1-specific primers which include forward primer 5’- GCCATCGCCGCCGCCGG-3’ and reverse primer 5’-GGGTCAGATCCATACCCGC-3’. These primers were used to amplify the Solanum tuberosum AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family due to the clade and high similarity it shared with other plant AMT1 genes. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1, and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th-10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: S. Salah, S. A. El-Masry, H. F. Sheba, R. A. El-Banna, W. Saad

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Background: Familial Mediterranean fever (FMF) has episodic or subclinical inflammation that may lead to a decrease in bone mineral density (BMD). Objective: To assess BMD in Egyptian children with FMF on genetic basis. Subjects and Methods: A cross sectional study included 45 FMF patients and 25 control children of both sexes, with age range between 3-16 years old. The patients were reclassified into 2 groups: Group I (A) 23 cases used colchicines for 1 month or less, and Group I (B) 22 cases used colchicines for more than 6 months. For both patients and control, MEFV mutations were defined using molecular genetics technique and BMD was measured by DXA at 2 sites: proximal femur and the lumber spines. Results: four frequent gene mutations were found in the patient group: E148Q (35.6%), V726A (33.3%), M680I (28.9.0%) and M694V (2.2%). There were also 4 heterozygous gene mutations in 40% of control children. Patients received colchicines treatment for less than 1 month had highly significant lower values of BMD at femur and lumber spines than control children (p<0.05). Patients received colchicines treatment for more than 6 months had improved values of BMD at femur compared to control, but there were still significant differences between them at lumbar spine (p>0.05). There are insignificant effect of type of gene mutation on BMD and the risk of osteopenia among the patients. Conclusion: FMF had significant effect on BMD. However, regular use of colchicines treatment improves this effect mainly at femur.

Keywords: familial mediterranean fever, bone mineral density, genes, children

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Zuzana Chaloupková, Zdeňka Marková, Václav Ranc, Radek Zbořil

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Prostate cancer is now one of the most serious oncological diseases in men with an incidence higher than that of all other solid tumors combined. Diagnosis of prostate cancer usually involves detection of related genes or detection of marker proteins, such as PSA. One of the new potential markers is PSMA (prostate specific membrane antigen). PSMA is a unique membrane bound glycoprotein, which is considerably overexpressed on prostate cancer as well as neovasculature of most of the solid tumors. Commonly applied methods for a detection of proteins include techniques based on immunochemical approaches, including ELISA and RIA. Magnetically assisted surface enhanced Raman spectroscopy (MA-SERS) can be considered as an interesting alternative to generally accepted approaches. This work describes a utilization of MA-SERS in a detection of PSMA in human blood. This analytical platform is based on magnetic nanocomposites Fe3O4@Ag, functionalized by a low-molecular selector labeled as JB303. The system allows isolating the marker from the complex sample using application of magnetic force. Detection of PSMA is than performed by SERS effect given by a presence of silver nanoparticles. This system allowed us to analyze PSMA in clinical samples with limits of detection lower than 1 ng/mL.

Keywords: diagnosis, cancer, PSMA, MA-SERS, Ag nanoparticles

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Authors: Peikun Zhang, Chunhua Cui

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Photoelectrochemical (PEC) water splitting provides a promising pathway to convert solar energy into renewable fuels. However, the main and seemingly insurmountable obstacle is that the sluggish kinetics of oxygen evolution reaction (OER) severely jeopardizes the overall efficiency, thus exploring highly active, stable, and appreciable catalysts is urgently requested. Herein a competitive coordination strategy was demonstrated to form a reversible hybrid homo-heterogeneous catalyst for efficient OER in alkaline media. The dynamic process involves an in-situ anchoring of soluble nickel–bipyridine pre-catalyst to a conductive substrate under OER and a re-dissolution course under open circuit potential, induced by the competitive coordination between nickel–bipyridine and nickel-hydroxyls. This catalyst allows to elaborately self-modulate a charge-transfer layer thickness upon the catalytic on-off operation, which affords substantially increased active sites, yet remains light transparency, and sustains the stability of over 200 hours of continuous operation. The integration of this catalyst with exemplified state-of-the-art Ni-sputtered Si photoanode can facilitate a ~250 mV cathodic shift at a current density of 20 mA cm-2. This finding helps the understanding of catalyst from a “dynamic” perspective, which represents a viable alternative to address remaining hurdles toward solar-driven water oxidation.

Keywords: molecular catalyst, oxygen evolution reaction, solar energy, transition metal complex, water splitting

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Authors: Nishal Parbhoo, John B. Dewar, Samantha Gildenhuys

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Rotavirus is the major cause of severe gastroenteritis worldwide in children aged 5 and younger. Death rates are high particularly in developing countries. The mature rotavirus is a non-enveloped triple-layered nucleocapsid containing 11 double-stranded RNA segments. Here a global view on the sequence and structure of the three main capsid proteins, VP7, VP6, and VP2 is taken by generating a consensus sequence for each of these rotavirus proteins, for each species obtained from published data of representative rotavirus genotypes from across the world and across species. The degree of conservation between species was represented on homology models for each of the proteins. VP7 shows the highest level of variation with 14 - 45 amino acids showing conservation of less than 60%. These changes are localized to the outer surface which is exposed to antibodies alluding to a possible mechanism in evading the immune system. The middle layer, VP6 shows lower variability with only 14-32 sites having lower than 70% conservation. The inner structural layer made up of VP2 showed the lowest variability with only 1-16 sites having less than 70% conservation across species. The results correlate with proteins’ multiple structural roles. Although the nucleotide sequences vary due to an error-prone replication and lack of proofreading, the corresponding amino acid sequence of VP2, 6 and 7 remains conserved. Sequence conservation maintained for the virus results in stable protein structures, fit for function. This can be exploited in drug design, molecular studies and biotechnological applications.

Keywords: amino acid sequence conservation, capsid protein, protein structure, vaccine candidate

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Authors: Cahit Demetgul, Sahin Bayraktar, Neslihan Beyazit

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Metalloenzymes are enzyme proteins containing metal ions, which are directly bound to the protein or to enzyme-bound nonprotein components. One of the major metalloenzymes that play a key role in oxidation reactions is catechol oxidase, which shows catecholase activity i.e. oxidation of a broad range of catechols to quinones through the four-electron reduction of molecular oxygen to water. Studies on the model compounds mimicking the catecholase activity are very useful and promising for the development of new, more efficient bioinspired catalysts, for in vitro oxidation reactions. In this study, a new tetradentate asymmetrical Schiff-base and its Cu(II) complex were synthesized by condensation of 4-nitro-1,2-phenylenediamine with 6-formyl-7-hydroxy-5-methoxy-2-methylbenzopyran-4-one and by using an appropriate Cu(II) salt, respectively. The prepared compounds were characterized by elemental analysis, FT-IR, NMR, UV-Vis and magnetic susceptibility. The catecholase-mimicking activity of the new Schiff Base Cu(II) complex was performed for the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) in methanol at 25 °C, where the electronic spectra were recorded at different time intervals. The yield of the quinone (3,5-DTBQ) was determined from the measured absorbance at 400 nm of the resulting solution. The compatibility of catalytic reaction with Michaelis-Menten kinetics was also investigated. In conclusion, we have found that our new Schiff Base Cu(II) complex presents a significant capacity to catalyze the oxidation reaction of the catechol to o-quinone.

Keywords: catecholase activity, Michaelis-Menten kinetics, Schiff base, transition metals

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Authors: M. J. Pourvaghar, M. E. Bahram

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Obesity and overweight is one of the most common metabolic disorders in industrialized countries and in developing countries. One consequence of pathological obesity is cardiovascular disease and metabolic syndrome. Chemerin is an adipocyne that plays a role in the regulation of the adipocyte function and the metabolism of glucose in the liver and musculoskeletal system. Most likely, chemerin is involved in obesity-related disorders such as type 2 diabetes and cardiovascular disease. Aerobic exercises reduce the level of chemerin and cause macrophage penetration into fat cells and inflammatory factors. Several efforts have been made to clarify the cellular and molecular mechanisms of hypertrophy and muscular atrophy. Myostatin, a new member of the TGF-β family, is a transforming growth factor β that its expression negatively regulates the growth of the skeletal muscle; and the increase of this hormone has been observed in conditions of muscular atrophy. While in response to muscle overload, its levels decrease after the atrophy period, TGF-β is the most important cytokine in the development of skeletal muscle. Myostatin plays an important role in muscle control, and animal and human studies show a negative role of myostatin in the growth of skeletal muscle. Separation of myostatin from Golgi begins on the ninth day of the onset period and continues until birth at all times of muscle growth. Higher levels of myostatin are found in obese people. Resistance training for 10 weeks could reduce levels of plasma myostatin.

Keywords: chemerin, myostatin, obesity, physical activity

Procedia PDF Downloads 294

Authors: Jiahui Song

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The application of an electric field can cause poration at cell membranes. This includes the outer plasma membrane, as well as the membranes of intracellular organelles. In order to analyze and predict such electroporation effects, it becomes necessary to first evaluate the electric fields and the transmembrane voltages. This information can then be used to assess changes in the pore formation energy that finally yields the pore distributions and their radii based on the Smolchowski equation. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into the pore formation energy equation. These changes make the pore formation energy E(r) self-adjusting in response to pore formation without causing uncontrolled growth and expansion. By using dynamic membrane tension, membrane electroporation in response to a 180kV/cm trapezoidal pulse with a 10 ns on time and 1.5 ns rise- and fall-times is discussed. Poration is predicted to occur at times beyond the peak at around 9.2 ns. Modeling also yields time-dependent distributions of the membrane pore population after multiple pulses. It shows that the pore distribution shifts to larger values of the radius with multiple pulsing. Molecular dynamics (MD) simulations are also carried out for a fixed field of 0.5 V/nm to demonstrate nanopore formation from a microscopic point of view. The result shows that the pore is predicted to be about 0.9 nm in diameter and somewhat narrower at the central point.

Keywords: high-intensity, nanosecond, dynamics, electroporation

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Authors: Jyoti Singh, Swati Dubey, Mukta Singh, R. P. Singh

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The freshwater microalgae Chlorella sp. is alluring considerable interest as a source for biofuel production due to its fast growth rate and high lipid content. Under nitrogen limited conditions, they can accumulate significant amounts of lipids. Thus, it is important to gain insight into the molecular mechanism of their lipid metabolism. In this study under nitrogen limited conditions, regular pattern of growth characteristics lipid accumulation and gene expression analysis of key regulatory genes of lipid biosynthetic pathway were carried out in microalgae Chlorella sp 3. Our results indicated that under nitrogen limited conditions there is a significant increase in the lipid content and lipid productivity, achieving 44.21±2.64 % and 39.34±0.66 mg/l/d at the end of the cultivation, respectively. Time-course transcript patterns of lipid biosynthesis genes i.e. acetyl coA carboxylase (accD) and diacylglycerol acyltransferase (dgat) showed that during late log phase of microalgae Chlorella sp.3 both the genes were significantly up regulated as compared to early log phase. Moreover, the transcript level of the dgat gene is two-fold higher than the accD gene. The results suggested that both the genes responded sensitively to the nitrogen limited conditions during the late log stage, which proposed their close relevance to lipid biosynthesis. Further, this transcriptome data will be useful for engineering microalgae species by targeting these genes for genetic modification to improve microalgal biofuel quality and production.

Keywords: biofuel, gene, lipid, microalgae

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Authors: Dilip Depan, Austin Simoneaux, William Chirdon, Ahmed Khattab

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In this study, we present a novel approach to synthesize polymer nanocomposites with nanohybrid shish-kebab architecture (NHSK). For this low-density and high density polyethylene (PE) was crystallized on various carbon nano-fillers using a novel and convenient method to prepare high-yield NHSK. Polymer crystals grew epitaxially on carbon nano-fillers using a solution crystallization method. The mixture of polymer and carbon fillers in xylene was flocculated and precipitated in ethanol to improve the product yield. Carbon nanofillers of varying diameter were also used as a nucleating template for polymer crystallization. The morphology of the prepared nanocomposites was characterized scanning electron microscopy (SEM), while differential scanning calorimetry (DSC) was used to quantify the amount of crystalline polymer. Interestingly, whatever the diameter of the carbon nanofiller is, the lamellae of PE is always perpendicular to the long axis of nanofiller. Surface area analysis was performed using BET. Our results indicated that carbon nanofillers of varying diameter can be used to effectively nucleate the crystallization of polymer. The effect of molecular weight and concentration of the polymer was discussed on the basis of chain mobility and crystallization capability of the polymer matrix. Our work shows a facile, rapid, yet high-yield production method to form polymer nanocomposites to reveal application potential of NHSK architecture.

Keywords: carbon nanotubes, polyethylene, nanohybrid shish-kebab, crystallization, morphology

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Authors: Muhammad H. Alu’datt, Inteaz Alli

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This study was conducted to prepare and evaluate the biological properties of protein co-precipitates from flaxseed and soybean. Protein was prepared by NaOH extraction through the mixing of soybean flour (Sf) and flaxseed flour (Ff) or mixtures of soybean extract (Se) and flaxseed extract (Fe). The protein co-precipitates were precipitated by isoelectric (IEP) and isoelectric-heating (IEPH) co-precipitation techniques. Effects of extraction and co-precipitation techniques on co-precipitate yield were investigated. Native-PAGE, SDS-PAGE were used to study the molecular characterization. Content and antioxidant activity of extracted free and bound phenolic compounds were evaluated for protein co-precipitates. Removal of free and bound phenolic compounds from protein co-precipitates showed little effects on the electrophoretic behavior of the proteins or the protein subunits of protein co-precipitates. Results showed that he highest protein contents and yield were obtained in for Sf-Ff/IEP co-precipitate with values of 53.28 and 25.58% respectively as compared to protein isolates and other co-precipitates. Results revealed that the Sf-Ff/IEP showed a higher content of bound phenolic compounds (53.49% from total phenolic content) as compared to free phenolic compounds (46.51% from total phenolic content). Antioxidant activities of extracted bound phenolic compounds with and without heat treatment from Sf-Ff/IEHP were higher as compared to free phenolic compounds extracted from other protein co-precipitates (29.68 and 22.84%, respectively).

Keywords: antioxidant, phenol, protein co-precipitate, yield

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Authors: Rini Rahul, Manoj Kumar

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Cadmium (Cd) is a poisonous trace metal, which is responsible for excess reactive oxygen species generation (ROS) in plants, thereby adversely affecting their productivity and commercial potential. Ricinus communis (castor) is an industry-efficient non-edible bioenergy crop used for phytoremediation and re-vegetation. We have determined the total Cd content in castor genotypes and established a relationship between the Cd tolerance mechanism and physiological parameters like chlorophyll fluorescence, the total photosynthetic activity, chlorophyll and carotenoid content as well as ROS generation and malondialdehyde content. This study is an effort to comprehend the interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), nicotianamine synthase (NAS) and Natural resistance-associated macrophage protein (NRAMP) gene. The antioxidant enzyme activity increased for WM hence conferring Cd toxicity in this genotype. RcNRAMP genes showed differential expression in GCH2 and WM genotypes; this can also be one of the reasons for Cd toxicity and sensitivity in WM and GCH2, respectively. The cause of pronounced Cd tolerance in WM leaves can be because of enhanced expression of RcNAS1, RcNAS2 and RcNAS3 genes. Our results demonstrate that there is an interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), NAS and NRAMP gene.

Keywords: ricinus communis, cadmium, reactive oxygen species, nicotianamine synthase, NRAMP, malondialdehyde

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Authors: Rizky Kusuma Cahyani

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Hepatitis B is a liver inflammatory disease caused by hepatitis B virus (HBV). This infection can be prevented by vaccination which contains HBV surface protein (sHBsAg). However, vaccine supply is limited. Several attempts have been conducted to produce local sHBsAg. However, the purity degree and protein yield are still inadequate. Therefore optimization of HBsAg purification steps is required to obtain high yield with better purification fold. In this study, optimization of purification was done in 2 steps, precipitation using variation of NaCl concentration (0,3 M; 0,5 M; 0,7 M) and PEG (3%, 5%, 7%); ion exchange chromatography (IEC) using NaCl 300-500 mM elution buffer concentration.To determine HBsAg protein, bicinchoninic acid assay (BCA) and enzyme-linked immunosorbent assay (ELISA) was used in this study. Visualization of HBsAg protein was done by SDS-PAGE analysis. Based on quantitative analysis, optimal condition at precipitation step was given 0,3 M NaCl and PEG 3%, while in ion exchange chromatography step, the optimum condition when protein eluted with NaCl 500 mM. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates that the presence of protein HBsAg with a molecular weight of 25 kDa (monomer) and 50 kDa (dimer). The optimum condition for purification of sHBsAg produced in Pichia pastoris gave a yield of 47% and purification fold 17x so that it would increase the production of hepatitis B vaccine to be more optimal.

Keywords: hepatitis B virus, HBsAg, hepatitis B surface antigen, Pichia pastoris, purification

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Authors: Jae Young Song, In-Ohk Ouh, Seyeon Park, Byeong Sul Kang, Soo Dong Cho, In-Soo Cho

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Canine parvovirus (CPV) is a major pathogen of diarrhea disease in dogs. CPV type 2 has three of antigenic variants such as 2a, 2b, and 2c. CPV constructs a small non-enveloped, icosahedral capsid that contains single-stranded DNA. It has capsids that two largely overlapping virion proteins (VP), VP1 (82 kDa), and VP2 (65 kDa). Baculoviruses are insect pathogens that regulate insect populations in nature and are being successfully used to control insect pests. The proteins produced in the baculovirus-expression system are used for instance for functional studies, vaccine preparations, or diagnostics. The vaccines produced by baculovirus-expression system showed elicitation of antibodies. The recombinant baculovirus infected SF9 cells showed broken shape. The recombinant VP2 proteins from cell pellet or supernatant were confirmed by western blotting. The result showed that the recombinant VP2 protein bands were appeared at 65 kDa molecular weight in both cell pellet and supernatant of infected SF9 cell. These results indicated that the recombinant baculovirus infected SF9 cell express the recombinant VP2 protein successfully. In addition, the expressed recombinant VP2 protein is secreted from cell to supernatant. The baculovirus expression system can be used to produce the VP2 protein of CPV 2c. In addition, the secretion property of the expression of VP2 protein may decrease the cost of production, because it can be skipped the cell breaking step. The produced VP2 protein could be used for vaccine and the agent of diagnostic tests. This study provides the foundation of the production of CPV 2c vaccine and the diagnostic agent.

Keywords: baculovirus, canine parvovirus 2c, dog, Korea

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Authors: Sonam Kumari

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Tuberculosis is the deadliest disease worldwide. Millions of people lose their lives every year due to this disease. It has turned lethal due to the erratic nature of its causative organism, Mycobacterium tuberculosis (Mtb). Mtb tends to enter into an inactive, dormant state and emerge to replicating state upon encountering favorable conditions. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes. Mtb has seven such proteins (WhiB1 to WhiB7). WhiB proteins are transcriptional regulators; they regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical parameters of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: mycobacterium tuberculosis, TB, whiB proteins, ITC

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Authors: Jiang Xu, Daoping Wang, Qun Li, Yinghong Pan

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2,4-Epibrassinolide (EBR), which is a kind of plant hormone Brassinosteroids (BRs), is widely studied and applied in the global scale but the proteomic characteristics of EBR alleviating low temperature stress in rice seedling leaves are still not clear. In this study, seeding rice of Nipponbare were treated with EBR and distilled water, then stressed at 4℃ or 26 ℃, and analyzed by mass spectrometry analysis, verified by parallel reaction monitoring technique (PRM). The results showed that 5778 proteins were identified in total and 4834 proteins were identified with quantitative information. Among them, 401 up-regulated and 220 down-regulated proteins may be related to EBR alleviating low temperature stress in rice seedling leaves. The molecular functions of most of up-regulated proteins are RNA binding and hydrolase activity and are mainly enriched in the pathways of carbon metabolism, folic acid synthesis, and amino acid biosynthesis. The down-regulated proteins are mainly related to catalytic activity and oxidoreductase activity and are mainly enriched in the pathways of limonene and pinene degradation, riboflavin metabolism, porphyrin and chlorophyll metabolism, and other metabolic pathways. PRM validation and literature analysis showed that NADP-malic acidase, peroxidase, 3-phosphoglycerate dehydrogenase, enolase, glyceraldehyde-3- phosphate dehydrogenase and pyruvate kinase are closely related to the effect of EBR on low temperature stress. These results also suggested that BRs could relieve the effect of low temperature stress on rice seed germination in many ways.

Keywords: 2, 4-Epibrassinolid, low temperature stress, proteomic analysis, rice

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Authors: Sergio Curilef, Boris Atenas

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Systems with long-range interactions are very common in nature. They are observed from the atomic scale to the astronomical scale and exhibit anomalies, such as inequivalence of ensembles, negative heat capacity, ergodicity breaking, nonequilibrium phase transitions, quasistationary states, and anomalous diffusion. These anomalies are exacerbated when special initial conditions are imposed; in particular, we use the so-called water bag initial conditions that stand for a uniform distribution. Several theoretical and practical implications are discussed here. A potential energy inspired by dipole-dipole interactions is proposed to build the dipole-type Hamiltonian mean-field model. As expected, the dynamics is novel and general to the behavior of systems with long-range interactions, which is obtained through molecular dynamics technique. Two plateaus sequentially emerge before arriving at equilibrium, which are corresponding to two different quasistationary states. The first plateau is a type of quasistationary state the lifetime of which depends on a power law of N and the second plateau seems to be a true quasistationary state as reported in the literature. The general behavior of the model according to its dynamics and thermodynamics is described. Using numerical simulation we characterize the mean kinetic energy, caloric curve, and the diffusion law through the mean square of displacement. The present challenge is to characterize the distributions in phase space. Certainly, the equilibrium state is well characterized by the Gaussian distribution, but quasistationary states in general depart from any Gaussian function.

Keywords: dipole-type interactions, dynamics and thermodynamics, mean field model, quasistationary states

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Authors: Summer Hassan, David Crossman

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Myocardial fibrosis (MF) has been loosely defined as the process occurring in the pathological remodeling of the myocardium due to excessive production and deposition of extracellular matrix (ECM) proteins, including collagen. This reduces tissue compliance and accelerates progression to heart failure, as well as affecting the electrical properties of the myocytes resulting in arrhythmias. Microscopic interrogation of MF is key to understanding the molecular orchestrators of disease. It is well-established that recruitment and stimulation of myofibroblasts result in Collagen deposition and the resulting expansion in the ECM. Many types of Collagens have been identified and implicated in scarring of tissue. In a series of experiments conducted at our lab, we aim to elucidate the role collagen VI plays in the development of myocardial fibrosis and its direct impact on myocardial function. This was investigated through an animal experiment in Rats with Collagen VI knockout diseased and healthy animals as well as Collagen VI wild diseased and healthy rats. Echocardiogram assessments of these rats ensued at four-time points, followed by microscopic interrogation of the myocardium aiming to correlate the role collagen VI plays in myocardial function. Our results demonstrate a deterioration in cardiac function as represented by the ejection fraction in the knockout healthy and diseased rats. This elucidates a potential protective role that collagen-VI plays following a myocardial insult. Current work is dedicated to the microscopic characterisation of the fibrotic process in all rat groups, with the results to follow.

Keywords: heart failure, myocardial fibrosis, collagen, echocardiogram, confocal microscopy

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Authors: Jia Xue, Frederica G. Lamar, Siyu Lin, Jennifer G. Lamori, Samendra Sherchan

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Brackish water samples from Lake Pontchartrain in Louisiana were assessed for the presence of pathogenic amoeba Naegleria fowleri, which causes primary amoebic meningoencephalitis (PAM). In our study, quantitative polymerase chain reaction (qPCR) methods were used to determine N. fowleri, E. coli, and Enterococcus in water collected from Lake Pontchartrain. A total of 158 water samples were analyzed over the 10-month sampling period. Statistically significant positive correlation between water temperature and N. fowleri concentration was observed. N. fowleri target sequence was detected at 35.4% (56/158) of the water samples from ten sites around the Lake ranged from 11.6 GC/100 ml water to 457.8 GC/100 ml water. A single factor (ANOVA) analysis shows the average concentration of N. fowleri in summer (119.8 GC/100 ml) was significantly higher than in winter (58.6 GC/100 ml) (p < 0.01). Statistically significant positive correlations were found between N. fowleri and qPCR E. coli results and N. fowleri and colilert E. coli (culture method), respectively. A weak positive correlation between E. coli and Enterococcus was observed from both qPCR (r = 0.27, p < 0.05) and culture based method (r = 0.52, p < 0.05). Meanwhile, significant positive correlation between qPCR and culture based methods for E. coli (r = 0.30, p < 0.05) and Enterococcus concentration was observed (r = 0.26, p < 0.05), respectively. Future research is needed to determine whether sediment is a source of N. fowleri found in the water column.

Keywords: brackish water, Escherichia coli, Enterococcus, Naegleria fowleri, primary amoebic meningoencephalitis (PAM), qPCR

Procedia PDF Downloads 146

Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

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Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: Morteza Haghi, Cigdem Yilmazbas, Ayse Zeynep Uysal, Melisa Tepedelen, Gozde Turkoz Bakirci

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Today, the increase in plastic waste accumulation is an inescapable consequence of environmental pollution; the disposal of these wastes has caused a significant problem. Variable methods have been utilized; however, biodegradation is the most environmentally friendly and low-cost method. Accordingly, the present study aimed to isolate the bacteria capable of biodegradation of plastics. In doing so, we applied the liquid carbon-free basal medium (LCFBM) prepared with deionized water for the isolation of bacterial species obtained from soil samples taken from the Izmir Menemen region. Isolates forming biofilms on plastic were selected and named (PLB3, PLF1, PLB1B) and subjected to a degradation test. FTIR analysis, 16s rDNA amplification, sequencing, identification of isolates were performed. Finally, at the end of the process, a mass loss of 16.6% in PLB3 isolate and 25% in PLF1 isolate was observed, while no mass loss was detected in PLB1B isolate. Only PLF1 and PLB1B created transparent zones on plastic texture. Considering the FTIR result, PLB3 changed plastic structure by 13.6% and PLF1 by 17%, while PLB1B did not change the plastic texture. According to the 16s rDNA sequence analysis, FLP1, PLB1B, and PLB3 isolates were identified as Streptomyces albogriseolus, Enterobacter cloacae, and Klebsiella pneumoniae, respectively.

Keywords: polyethylene, biodegradation, bacteria, 16s rDNA, FTIR

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Authors: Sabitha Rani A., Nagamani V.

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Embelia ribes Burm.f (Family-Myrsinaceae) commonly known as Vidanga or Baibirang, is one of the important medicinal plants of India. The seed extract is reported to be antidiabetic, antitumour, analgesic, anti-inflammatory, antispermatogenic, free radical scavenging activities and widely used in more than 75 Ayurvedic commercial formulations. Among the 100 different species of Embelia, E. ribes is considered as a major source of Embelin, a bioactive compound. Because of high demand and low availability, the seeds of E. ribes are substituted with many cheaper alternatives. Therefore, the present study of RAPD-PCR analysis was undertaken to develop molecular markers for identification of E. ribes. A total of 13 different seed samples of Embelia were collected from different agro-climatic regions of India. The seeds of E.ribes were collected from Kalpetta, Kerala and three different seed samples were collected from traders of Odisha, Madhya Pradesh, Maharastra. The other nine seed samples were collected from local traders which they have collected from different regions of India. Genomic DNA was isolated from different seed samples E. ribes and RAPD-PCR was performed on 13 different seed samples using 47 random primers. Out of all the primers, only 22 primers produced clear and highly-reproducible banding patterns. The 22 selected RAPD primers generated a total of 280 alleles with an average of 12 alleles per primer pair. In the present study, we have identified three RAPD-PCR markers i.e. OPF5_480 bp, OPH11_520 bp and OPH4_530 bp which can be used for genetic fingerprinting of E. ribes. This methodology can be employed for identification of original E. ribes and also distinguishing it from other substitutes and adulterants.

Keywords: Embelia ribes, RAPD-PCR, primers, genetic analysis

Procedia PDF Downloads 281

Authors: Sara Gardideh, Mansoor Barati

Abstract:

The mineral carbonation approach for reducing global warming has garnered interest on a worldwide scale. Due to the benefits of permanent storage and abundant mineral resources, mineral carbonation (MC) is one of the most effective strategies for sequestering CO₂. The combination of mineral processing for primary metal recovery and mineral carbonation for carbon sequestration is an emerging field of study with the potential to minimize capital costs. A detailed study of low-pressures–solid carbonation of ultramafic tailings in a dry environment has been accomplished. In order to track the changing structure of serpentine minerals and their reactivity as a function of temperature (300-900 ᵒC), CO₂ partial pressure (25-90 mol %), and thermal preconditioning, thermogravimetry has been utilized. The incongruent CO₂ van der Waals molecular diameters with the octahedral-tetrahedral lattice constants of serpentine were used to explain the mild carbonation reactivity. Serpentine requires additional thermal-treatment to remove hydroxyl groups, resulting in the chemical transformation to pseudo-forsterite, which is a mineral composed of isolated SiO₄ tetrahedra linked by octahedrally coordinated magnesium ions. The heating treatment above 850 ᵒC is adequate to remove chemically bound water from the lattice. Particles with a diameter < 34 (μm) are desirable, and thermally treated serpentine at 850 ᵒC for 2.30 hours reached 65% CO₂ storage capacity. The decrease in particle size, increase in temperature, and magnetic separation can dramatically enhance carbonation.

Keywords: particle size, thermogravimetry, thermal-treatment, serpentine

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Authors: Debadi Chakraborty, John E. Sader

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Nanomechanical devices have emerged as a versatile platform for a host of applications due to their extreme sensitivity to environmental conditions. For example, mass measurements with sensitivity at the atomic level have recently been demonstrated. Ultrafast laser spectroscopy coherently excite the vibrational modes of metal nanoparticles and permits precise measurement of the vibration characteristics as a function of nanoparticle shape, size and surrounding environment. This study reports that the vibration of metal nanoparticles in simple liquids, like water and glycerol are not described by conventional fluid mechanics, i.e., Navier Stokes equations. The intrinsic molecular relaxation processes in the surrounding liquid are found to have a profound effect on the fluid-structure interaction of mechanical devices at nanometre scales. Theoretical models have been developed based on the non-Newtonian viscoelastic fluid-structure interaction theory to investigate the vibration of nanoparticles immersed in simple fluids. The utility of this theoretical framework is demonstrated by comparison to measurements on single nanowires and ensembles of metal rods. This study provides a rigorous foundation for the use of metal nanoparticles as ultrasensitive mechanical sensors in fluid and opens a new paradigm for understanding extremely high frequency fluid mechanics, nanoscale sensing technologies, and biophysical processes.

Keywords: fluid-structure interaction, nanoparticle vibration, ultrafast laser spectroscopy, viscoelastic damping

Procedia PDF Downloads 255

Authors: Junie B. Billones, Maria Constancia O. Carrillo, Voltaire G. Organo, Stephani Joy Y. Macalino, Inno A. Emnacen, Jamie Bernadette A. Sy

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One of the major interferences in the Philippines’ tuberculosis control program is the widespread prevalence of Mtb strains that are resistant to known drugs, such as the MDR-TB (Multi Drug Resistant Tuberculosis) and XDR-TB (Extensively Drug Resistant Tuberculosis). Therefore, there is a pressing need to search for novel Mtb drug targets in order to be able to combat these drug resistant strains. The enzyme 7,8-diaminopelargonic acid aminotransferase enzyme, or more commonly known as BioA, is one such ideal target, as it is known that humans do not possess this enzyme. BioA primarily plays a key role in Mtb’s lipid biosynthesis pathway; more specifically in the synthesis of the enzyme cofactor biotin. In this study, structure-based pharmacophore screening, docking, and ADMET evaluation of compounds obtained from the DrugBank chemical database were performed against the MtbBioA enzyme. Results of the screening, docking, ADMET, and TOPKAT calculations revealed that out of the 6,516 compounds in the library, only 7 compounds indicated more favorable binding energies as compared to the enzyme’s known inhibitor, amiclenomycin (ACM), as well as good solubility and toxicity properties. Moreover, out of these 7 compounds, Molecule 6 exhibited the best solubility and toxicity properties. In the future, these lead compounds may then be subjected to bioactivity assays in vitro or in vivo for further evaluation of its therapeutic efficacy.

Keywords: 7, 8-diaminopelargonic acid aminotransferase, BioA, pharmacophore, molecular docking, ADMET, TOPKAT

Procedia PDF Downloads 438