Search results for: molecular biology

Authors: A. Kalaei, A. H. W. Ngan

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In this study, a mesoscopic continuum dislocation dynamics (CDD) approach is applied to simulate the intergranular slip transfer. The CDD scheme applies an efficient kinematics equation to model the evolution of the “all-dislocation density,” which is the line-length of dislocations of each character per unit volume. As the consideration of every dislocation line can be a limiter for the simulation of slip transfer in large scales with a large quantity of participating dislocations, a coarse-grained, extensive description of dislocations in terms of their density is utilized to resolve the effect of collective motion of dislocation lines. For dynamics closure, namely, to obtain the dislocation velocity from a velocity law involving the effective glide stress, mutual elastic interaction of dislocations is calculated using Mura’s equation after singularity removal at the core of dislocation lines. The developed scheme for slip transfer can therefore resolve the effects of the elastic interaction and pile-up of dislocations, which are important physics omitted in coarser models like crystal plasticity finite element methods (CPFEMs). Also, the length and timescales of the simulationareconsiderably larger than those in molecular dynamics (MD) and discrete dislocation dynamics (DDD) models. The present work successfully simulates that, as dislocation density piles up in front of a grain boundary, the elastic stress on the other side increases, leading to dislocation nucleation and stress relaxation when the local glide stress exceeds the operation stress of dislocation sources seeded on the other side of the grain boundary. More importantly, the simulation verifiesa phenomenological misorientation factor often used by experimentalists, namely, the ease of slip transfer increases with the product of the cosines of misorientation angles of slip-plane normals and slip directions on either side of the grain boundary. Furthermore, to investigate the effects of the critical stress-intensity factor of the grain boundary, dislocation density sources are seeded at different distances from the grain boundary, and the critical applied stress to make slip transfer happen is studied.

Keywords: grain boundary, dislocation dynamics, slip transfer, elastic stress

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Authors: Supriya Gupta, Paresh Chokshi

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Polymer-particle interactions can be effectively utilized to produce composites that possess physicochemical properties superior to that of neat polymer. The incorporation of fillers with dimensions comparable to polymer chain size produces composites with extra-ordinary properties owing to very high surface to volume ratio. The dispersion of nanoparticles is achieved by inducing steric repulsion realized by grafting particles with polymeric chains. A comprehensive understanding of the interparticle interaction between these functionalized nanoparticles plays an important role in the synthesis of a stable polymer nanocomposite. With the focus on incorporation of clay sheets in a polymer matrix, we theoretically construct the polymer mediated interparticle potential for two nanosheets grafted with polymeric chains. The self-consistent field theory (SCFT) is employed to obtain the inhomogeneous composition field under equilibrium. Unlike the continuum models, SCFT is built from the microscopic description taking in to account the molecular interactions contributed by both intra- and inter-chain potentials. We present the results of SCFT calculations of the interaction potential curve for two grafted nanosheets immersed in the matrix of polymeric chains of dissimilar chemistry to that of the grafted chains. The interaction potential is repulsive at short separation and shows depletion attraction for moderate separations induced by high grafting density. It is found that the strength of attraction well can be tuned by altering the compatibility between the grafted and the mobile chains. Further, we construct the interaction potential between two nanosheets grafted with diblock copolymers with one of the blocks being chemically identical to the free polymeric chains. The interplay between the enthalpic interaction between the dissimilar species and the entropy of the free chains gives rise to a rich behavior in interaction potential curve obtained for two separate cases of free chains being chemically similar to either the grafted block or the free block of the grafted diblock chains.

Keywords: clay nanosheets, polymer brush, polymer nanocomposites, self-consistent field theory

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Authors: Kyung Jin Kim, Jiwon Kwak, Jae-Hoon Lee, Soo Suk Lee

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MicroRNAs (miRNA) are a class of endogenous, single-stranded, small, and non-protein coding RNA molecules typically 20-25 nucleotides long. They are thought to regulate the expression of other genes in a broad range by binding to 3’- untranslated regions (3’-UTRs) of specific mRNAs. The detection of miRNAs is very important for understanding of the function of these molecules and in the diagnosis of variety of human diseases. However, detection of miRNAs is very challenging because of their short length and high sequence similarities within miRNA families. So, a simple-to-use, low-cost, and highly sensitive method for the detection of miRNAs is desirable. In this study, we demonstrate a novel bi-directional extension (BDE) assay. In the first step, a specific linear RT primer is hybridized to 6-10 base pairs from the 3’-end of a target miRNA molecule and then reverse transcribed to generate a cDNA strand. After reverse transcription, the cDNA was hybridized to the 3’-end which is BDE sequence; it played role as the PCR template. The PCR template was amplified in an SYBR green-based quantitative real-time PCR. To prove the concept, we used human brain total RNA. It could be detected quantitatively in the range of seven orders of magnitude with excellent linearity and reproducibility. To evaluate the performance of BDE assay, we contrasted sensitivity and specificity of the BDE assay against a commercially available poly (A) tailing method using miRNAs for let-7e extracted from A549 human epithelial lung cancer cells. The BDE assay displayed good performance compared with a poly (A) tailing method in terms of specificity and sensitivity; the CT values differed by 2.5 and the melting curve showed a sharper than poly (A) tailing methods. We have demonstrated an innovative, cost-effective BDE assay that allows improved sensitivity and specificity in detection of miRNAs. Dynamic range of the SYBR green-based RT-qPCR for miR-145 could be represented quantitatively over a range of 7 orders of magnitude from 0.1 pg to 1.0 μg of human brain total RNA. Finally, the BDE assay for detection of miRNA species such as let-7e shows good performance compared with a poly (A) tailing method in terms of specificity and sensitivity. Thus BDE proves a simple, low cost, and highly sensitive assay for various miRNAs and should provide significant contributions in research on miRNA biology and application of disease diagnostics with miRNAs as targets.

Keywords: bi-directional extension (BDE), microRNA (miRNA), poly (A) tailing assay, reverse transcription, RT-qPCR

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Authors: Aidan Battison, Neliswa Mama

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Environmental pollution by ionic species has been identified as one of the biggest challenges to the sustainable development of communities. The widespread use of organic and inorganic chemical products and the release of toxic chemical species from industrial waste have resulted in a need for advanced monitoring technologies for environment protection, remediation and restoration. Some of the disadvantages of conventional sensing methods include expensive instrumentation, well-controlled experimental conditions, time-consuming procedures and sometimes complicated sample preparation. On the contrary, the development of fluorescent chemosensors for biological and environmental detection of metal ions has attracted a great deal of attention due to their simplicity, high selectivity, eidetic recognition, rapid response and real-life monitoring. Coumarin derivatives S1 and S2 (Scheme 1) containing 1,2,3-triazole moieties at position -3- have been designed and synthesized from azide and alkyne derivatives by CuAAC “click” reactions for the detection of metal ions. These compounds displayed a strong preference for Fe3+ ions with complexation resulting in fluorescent quenching through photo-induced electron transfer (PET) by the “sphere of action” static quenching model. The tested metal ions included Cd2+, Pb2+, Ag+, Na+, Ca2+, Cr3+, Fe3+, Al3+, Cd2+, Ba2+, Cu2+, Co2+, Hg2+, Zn2+ and Ni2+. The detection limits of S1 and S2 were determined to be 4.1 and 5.1 uM, respectively. Compound S1 displayed the greatest selectivity towards Fe3+ in the presence of competing for metal cations. S1 could also be used for the detection of Fe3+ in a mixture of CH3CN/H¬2¬O. Binding stoichiometry between S1 and Fe3+ was determined by using both Jobs-plot and Benesi-Hildebrand analysis. The binding was shown to occur in a 1:1 ratio between the sensor and a metal cation. Reversibility studies between S1 and Fe3+ were conducted by using EDTA. The binding site of Fe3+ to S1 was determined by using 13 C NMR and Molecular Modelling studies. Complexation was suggested to occur between the lone-pair of electrons from the coumarin-carbonyl and the triazole-carbon double bond.

Keywords: chemosensor, "click" chemistry, coumarin, fluorescence, static quenching, triazole

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Authors: Sher Mohammed, Purushottam Lal, Pawan K. Kasera

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The Thar Desert of Rajasthan covers a wide geographical area spreading between 23.3° to 30.12°, North latitude and 69.3◦ to 76◦ Eastern latitudes; having a unique spectrum of arid zone vegetation. This desert is spreading over 12 districts having a rich source of economically important/threatened plant diversity interacting and growing with adverse climatic conditions of the area. Due to variable geological, physiographic, climatic, edaphic and biotic factors, the arid zone medicinal flora exhibit a wide collection of angiosperm families. The herbal diversity of this arid region is medicinally important in household remedies among tribal communities as well as in traditional systems. The on-going increasing disturbances in natural ecosystems are due to climatic and biological, including anthropogenic factors. The unique flora and subsequently dependent faunal diversity of the desert ecosystem is losing its biotic potential. A large number of plants have no future unless immediate steps are taken to arrest the causes, leading to their biological improvement. At present the potential loss in ecological amplitude of various genera and species is making several plant species as red listed plants of arid zone vegetation such as Commmiphora wightii, Tribulus rajasthanensis, Calligonum polygonoides, Ephedra foliata, Leptadenia reticulata, Tecomella undulata, Blepharis sindica, Peganum harmala, Sarcostoma vinimale, etc. Mostly arid zone species are under serious pressure against prevailing ecosystem factors to continuation their life cycles. Genetic, molecular, cytological, biochemical, metabolic, reproductive, germination etc. are the several points where the floral diversity of the arid zone area is facing severe ecological influences. So, there is an urgent need to conserve them. There are several opportunities in the field to carry out remarkable work at particular levels to protect the native plants in their natural habitat instead of only their in vitro multiplication.

Keywords: ecology, evaluation, xerophytes, economically, threatened plants, conservation

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Authors: Muhammad Imran, Sarfraz Shafiq, Xiangru Tang

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Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcripts variability and proteome diversity in plants. Fragrant rice (Oryza sativa L.) has a high economic and nutritional value, and the application of micronutrients regulate 2-acetyl-1-pyrroline (2-AP) production, which is responsible for aroma in fragrant rice. However, no systematic investigation of AS events in response to micronutrients (Zn) has been performed in fragrant rice. Furthermore, the post-transcriptional regulation of genes involved in 2-AP biosynthesis is also not known. In this study, a comprehensive analysis of AS events under two gradients of Zn treatment in two different fragrant rice cultivars (Meixiangzhan-2 and Xiangyaxiangzhan) was performed. A total of 386 and 598 significant AS events were found in Meixiangzhan-2 treated with low and high doses of Zn, respectively. In Xiangyaxiangzhan, a total of 449 and 598 significant AS events were found in low and high doses of Zn, respectively. Go analysis indicated that these genes were highly enriched in physiological processes, metabolism, and cellular process in both cultivars. However, genotype and dose-dependent AS events were also detected in both cultivars. By comparing differential AS (DAS) events with differentially expressed genes (DEGs), we found a weak overlap among DAS and DEGs in both fragrant rice cultivars, indicating that only a few genes are post-transcriptionally regulated in response to Zn treatment. We further report that Zn differentially regulates the expression of 2-AP biosynthesis-related genes in both cultivars, and Zn treatment altered the editing frequency of SNPs in the genes involved in 2-AP biosynthesis. Finally, we showed that epigenetic modifications associated with active gene transcription are generally enriched over 2-AP biosynthesis-related genes. Taken together, our results provide evidence of the post-transcriptional gene regulation in fragrant rice in response to Zn treatment and highlight that the 2-AP biosynthesis pathway may also be post-transcriptionally regulated through epigenetic modifications. These findings will serve as a cornerstone for further investigation to understand the molecular mechanisms of 2-AP biosynthesis in fragrant rice.

Keywords: fragrant rice, 2-acetyl-1-pyrroline, gene expression, zinc, alternative splicing, SNPs

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Authors: Onuoha Ogbonnaya Gideon, Ishaq Hafsah Yusuf

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Introduction: Meat is a perishable food of good nutrition. Meat ranks among the most significant, nutritious, and favored food items available to most locals. It is a good source of protein (17-19%), depending on sources, and contains appreciable amounts of fat and moisture. However, it has a very short shelf life due mainly to its high moisture, fat, and other nutrient contents. Meat spoilage can result from microbial proliferation as well as inherent enzymes in the meat tissues. Bacteria contamination and permeability to both oxygen and water vapor are major concerns associated with spoilage of meat and its storage. Packaging is fundamental in the preservation and presentation of food. Red clay is a very common substance; hydrous aluminum phyllosilicate, sometimes with varying amounts of iron, magnesium, alkali metals, alkaline earth, and cation formed from sedimentary rocks. Furthermore, red clay is an extremely absorbent material and develops plasticity when wet due to the molecular film of water surrounding the clay particles but can become hard, impervious, brittle, and non-brittle and non-plastic when dry. In developing countries, the high cost of refrigeration technologies and most other methods of preserving meat are exorbitant and thus can be substituted with the less expensive and readily available red clay for the preservation of meat. Methodology: 1000g of lean meat was diced into cubes of 10g each. The sample was then divided into four groups labelled raw meat (RMC); raw in 10% brine solution (RMB), boiled meat (BMC), and fried meat (FMC). It was then encapsulated with 2mm thick red clay and then heated in a muffle furnace at a temperature of 600OC for 30min. The samples were kept on a bench top for 30 days, and a storage study was carried out. Results: Our findings showed a decrease in value during storage for the physiochemical properties of all the sample; pH values decreased [RMC (7.05-7.6), RMB (8.46-7.0), BMC (6.0-5.0), FMC (4.08-3.9)]; free fatty acid content decreased with storage time [RMC (32.6%-31%), RMB (30.2%-28.6%), BMC (30.5%-27.4%), FMC (25.6%-23.8%)]; total soluble solid value decreased [RMC16.20-15.07, RMB (17.22-16.04), BMC (17.05-15.54), FMC (15.3-14.9)]. Conclusion: This result shows that encapsulation with red clay reduced all the values analyzed and thus has the potential to extend the shelf life of stored meat.

Keywords: red clay, encapsulating, shelf life, physicochemical properties, lean meat

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Authors: Sarocha Vivatvakin, Thanaporn Ratchataswan, Thiratest Leesutipornchai, Komkrit Ruangritchankul, Somboon Keelawat, Virachai Kerekhanjanarong, Patnarin Mahattanasakul, Saknan Bongsebandhu-Phubhakdi

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In this globalization era, much attention has been drawn to various molecular biomarkers, which may have the potential to predict the progression of cancer. Epidermal growth factor receptor (EGFR) is the classic member of the ErbB family of membrane-associated intrinsic tyrosine kinase receptors. EGFR expression was found in several organs throughout the body as its roles involve in the regulation of cell proliferation, survival, and differentiation in normal physiologic conditions. However, anomalous expression, whether over- or under-expression is believed to be the underlying mechanism of pathologic conditions, including carcinogenesis. Even though numerous discussions regarding the EGFR as a prognostic tool in head and neck cancer have been established, the consensus has not yet been met. The aims of the present study are to assess the correlation between the level of EGFR expression and demographic data as well as clinicopathological features and to evaluate the ability of EGFR as a reliable prognostic marker. Furthermore, another aim of this study is to investigate the probable pathophysiology that explains the finding results. This retrospective study included 30 squamous cell laryngeal carcinoma patients treated at King Chulalongkorn Memorial Hospital from January 1, 2000, to December 31, 2004. EGFR expression level was observed to be significantly downregulated with the progression of the laryngeal cancer stage. (one way ANOVA, p = 0.001) A statistically significant lower EGFR expression in the late stage of the disease compared to the early stage was recorded. (unpaired t-test, p = 0.041) EGFR overexpression also showed the tendency to increase recurrence of cancer (unpaired t-test, p = 0.128). A significant downregulation of EGFR expression was documented in advanced stage laryngeal cancer. The results indicated that EGFR level correlates to prognosis in term of stage progression. Thus, EGFR expression might be used as a prevailing biomarker for laryngeal squamous cell carcinoma prognostic prediction.

Keywords: downregulation, epidermal growth factor receptor, immunohistochemistry, laryngeal squamous cell carcinoma

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Authors: Satendra Pal Singh, Dalip Kr. Kakru, Jyoti Mishra, Rajesh Thakur, Tarana Sarwat

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COVID-19 is still an intrigue as far as morbidity or mortality is concerned. The rate of recovery varies from person to person, & it depends upon the accessibility of the healthcare system and the roles played by the physicians and caregivers. It is envisaged that with the passage of time, people would become immune to this virus, and those who are vulnerable would sustain themselves with the help of vaccines. The proposed study deals with the severeness of COVID-19 is associated with some specific biomarkers linked to correlate age and gender. We will be assessing the overall homeostasis of the persons who were affected by the coronavirus infection and also of those who recovered from it. Some people show more severe effects, while others show very mild symptoms, however, they show low CT values. Thus far, it is unclear why the new strain of Covid has different effects on different people in terms of age, gender, and ABO blood typing. According to data, the fatality rate with heart disease was 10.5 percent, 7.3 percent were diabetic, and 6 percent who are already infected from other comorbidities. However, some COVID-19 cases are worse than others & it is not fully explainable as of date. Overall data show that the ABO blood group is effective or prone to the risk of SARS-COV2 infection, while another study also shows the phenotypic effects of the blood group related to covid. It is an accepted fact that females have more strong immune systems than males, which may be related to the fact that females have two ‘X’ chromosomes, which might contain a more effective immunity booster gene on the X chromosome, and are capable to protect the female. Also specific sex hormones also induce a better immune response in a specific gender. This calls for in-depth analysis to be able to gain insight into this dilemma. COVID-19 is still not fully characterized, and thus we are not very familiar with its biology, mode of infection, susceptibility, and overall viral load in the human body. How many virus particles are needed to infect a person? How, then, comorbidity contribute to coronavirus infection? Since the emergence of this virus in 2020, a large number of papers have been published, and seemingly, vaccines have been prepared. But still, a large number of questions remain unanswered. The proneness of humans for infection by covid-19 needs to be established to be able to develop a better strategy to fight this virus. Our study will be on the Impact of demography on the Severity of covid-19 infection & at the same time, will look into gender-specific sensitivity of Covid-19 and the Operational variation of different biochemical markers in Covid-19 positive patients. Besides, we will be studying the co-relation, if any, of COVID severity & ABO Blood group type and the occurrence of the most common blood group type amongst positive patience.

Keywords: coronavirus, ABO blood group, age, gender

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Authors: Jasbir Singh, Devender Kumar, Davender Redhu, Surender Kumar, Vandana Bhardwaj

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Single Nucleotide polymorphism (SNP) of proteosomal gene complex is involved in the pathogenesis of hepatitis B Virus (HBV) infection. Some of such proteosomal gene complex are large multifunctional proteins (LMP) and antigen associated transporters that help in antigen presentation. Both are involved in intracellular processing and presentation of viral antigens in association with Major Histocompatability Complex (MHC) Class I molecules. A total of hundred each of hepatitis B virus infected and control samples from northern India were studied. Genomic DNA was extracted from all studied samples and PCR-RFLP method was used for genotyping at different positions of LMP genes. Genotypes at a given position were inferred from the pattern of bands and genotype frequencies and haplotype frequencies were also calculated. Homozygous SNP {A>C} was observed at codon 145 of LMP7 gene and having a protective role against HBV as there was statistically significant high distribution of this SNP among controls than cases. Heterozygous SNP {A>C} was observed at codon 145 of LMP7 gene and made individuals more susceptible to HBV infection as there was statistically significant high distribution of this SNP among cases than control. SNP {T>C} was observed at codon 60 of LMP2 gene but statistically significant differences were not observed among controls and cases. For codon 145 of LMP7 and codon 60 of LMP2 genes, four haplotypes were constructed. Haplotype I (LMP2 ‘C’ and LMP7 ‘A’) made individuals carrying it more susceptible to HBV infection as there was statistically significant high distribution of this haplotype among cases than control. Haplotype II (LMP2 ‘C’ and LMP7 ‘C’) made individuals carrying it more immune to HBV infection as there was statistically significant high distribution of this haplotype among control than cases. Thus it can be concluded that homozygous SNP {A>C} at codon 145 of LMP7 and Haplotype II (LMP2 ‘C’ and LMP7 ‘C’) has a protective role against HBV infection whereas heterozygous SNP {A>C} at codon 145 of LMP7 and Haplotype I (LMP2 ‘C’ and LMP7 ‘A’) made individuals more susceptible to HBV infection.

Keywords: Hepatitis B Virus, single nucleotide polymorphism, low molecular weight proteins, transporters associated with antigen presentation

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Authors: A. T. Toci, M. V. B. Zanoni

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The advanced oxidation processes have been defined as destructive technologies treatment of wastewater. These involve the formation of powerful oxidizing agents (usually hydroxyl radical .OH) capable of reacting with organic compounds present in wastewater, transforming damaging substances in CO2 and H2O (mineralization) or other innocuous products. However, the photochemical degradation with singlet oxygen has been little explored as oxidative pathway for the treatment of effluents containing food colorants. The molecular oxygen is an effective suppressor of organic molecules in the triplet excited state. One of the possible results of the physical withdrawal is the formation of singlet oxygen. Studies with singlet oxygen (1O2) show an high reactivity of the excited state of the molecule with olefins, aromatic hydrocarbons and a number of other organic and inorganic compounds. Its reactivity is about 2500 times larger than the oxygen in the ground state. Thus, in this work, it was studied the degradation of some dyes used in food industry (tartrazine, sunset yellow, erythrosine and carmoisine) by singlet oxygen. The sensitizer used for generating the 1O2 was methylene blue, which has a quantum yield generation of 0.50. Samples were prepared in water at a concentration of 5 ppm and irradiated with a sunlight simulator (Newport brand, model no. 67005) by consecutive 8h. The absorption spectra of UV-Vis molecules were made each hour irradiation. The degradation kinetics for each dye was determined using the maximum length of each dye absorption. The analysis by UV-Vis revealed that the processes were very efficient for the colorants sunset yellow and carmoisine. Both presented degradation kinetics of order zero with degradation constants 0.416 and 0.104, respectively. In the case of sunset yellow degradation reached 53% after 7h irradiation, Demonstrating the process efficiency. The erithrosine presented during the period irradiated a oscillating degradation kinetics, which requires further study. In the other hand, tartrazine was stable in the presence of 1O2. The investigation of the dyes degradation products owned degradation by 1O2 are underway, the techniques used for this are MS and NMR. The results of this study will enable the application of the cleanest methods for the treatment of industrial effluents, as there are other non-toxic and polluting molecules to generate 1O2.

Keywords: food colourants, singlet oxygen, degradation, wastewater, oxidative

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Authors: Juan Li, Hui Tian, Min Wang

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In China, under the considerable pressure of 'Gaokao' –the highly competitive college entrance examination, high school teachers and parents often worry that doing physical activity would take away the students’ precious study time and may have a negative impact on the academic grades. There was a tendency to achieve high academic scores at the cost of physical exercise. Therefore, the purpose of this study was to examine the relationship between the physical fitness and academic achievement of Chinese high school students. The participants were 968 grade one (N=457) and grade two students (N=511) with an average age of 16 years from three high schools of different levels in Beijing, China. 479 were boys, and 489 were girls. One of the schools is a top high school in China, another is a key high school in Beijing, and the other is an ordinary high school. All analyses were weighted using SAS 9.4 to ensure the representatives of the sample. The weights were based on 12 strata of schools, sex, and grades. Physical fitness data were collected using the scores of the National Physical Fitness Test, which is an annual official test administered by the Ministry of Education in China. It includes 50m run, sits and reach test, standing long jump, 1000m run (for boys), 800m run (for girls), pull-ups for 1 minute (for boys), and bent-knee sit-ups for 1 minute (for girls). The test is an overall evaluation of the students’ physical health on the major indexes of strength, endurance, flexibility, and cardiorespiratory function. Academic scores were obtained from the three schools with the students’ consent. The statistical analysis was conducted with SPSS 24. Independent-Samples T-test was used to examine the gender group differences. Spearman’s Rho bivariate correlation was adopted to test for associations between physical test results and academic performance. Statistical significance was set at p<.05. The study found that girls obtained higher fitness scores than boys (p=.000). The girls’ physical fitness test scores were positively associated with the total academic grades (rs=.103, p=.029), English (rs=.096, p=.042), physics (rs=.202, p=.000) and chemistry scores (rs=.131, p=.009). No significant relationship was observed in boys. Cardiorespiratory fitness had a positive association with physics (rs=.196, p=.000) and biology scores (rs=.168, p=.023) in girls, and with English score in boys (rs=.104, p=.029). A possible explanation for the greater association between physical fitness and academic achievement in girls rather than boys was that girls showed stronger motivation in achieving high scores in whether academic tests or fitness tests. More driven by the test results, girls probably tended to invest more time and energy in training for the fitness test. Higher fitness levels were associated with an academic benefit among girls generally in Chinese high schools. Therefore, physical fitness needs to be given greater emphasis among Chinese adolescents and gender differences need to be taken into consideration.

Keywords: physical fitness; adolescents; academic achievement; high school

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Authors: Kan Yu, Khui Hung Lee, Eben Afrifa-Yamoah, Jing Guo, Katrina Harrison, Jack Goldblatt, Nicholas Pachter, Jitian Xiao, Guicheng Brad Zhang

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Background and Significance of the Study: Congenital Heart Defects (CHDs) are the most common malformation at birth and one of the leading causes of infant death. Although the exact etiology remains a significant challenge, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of congenital heart defects. At present, no existing DNA methylation biomarkers are used for early detection of CHDs. The existing CHD diagnostic techniques are time-consuming and costly and can only be used to diagnose CHDs after an infant was born. The present study employed a machine learning technique to analyse genome-wide methylation data in children with and without CHDs with the aim to find methylation biomarkers for CHDs. Methods: The Illumina Human Methylation EPIC BeadChip was used to screen the genome‐wide DNA methylation profiles of 24 infants diagnosed with congenital heart defects and 24 healthy infants without congenital heart defects. Primary pre-processing was conducted by using RnBeads and limma packages. The methylation levels of top 600 genes with the lowest p-value were selected and further investigated by using a random forest approach. ROC curves were used to analyse the sensitivity and specificity of each biomarker in both training and test sample sets. The functionalities of selected genes with high sensitivity and specificity were then assessed in molecular processes. Major Findings of the Study: Three genes (MIR663, FGF3, and FAM64A) were identified from both training and validating data by random forests with an average sensitivity and specificity of 85% and 95%. GO analyses for the top 600 genes showed that these putative differentially methylated genes were primarily associated with regulation of lipid metabolic process, protein-containing complex localization, and Notch signalling pathway. The present findings highlight that aberrant DNA methylation may play a significant role in the pathogenesis of congenital heart defects.

Keywords: biomarker, congenital heart defects, DNA methylation, random forest

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Authors: Isabella Lima Leite de Freitas

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The importance of astronomy for humanity is unquestionable. Despite being a robust science, capable of bringing new discoveries every day and quickly increasing the ability of researchers to understand the universe more deeply, scientific research in this area can also help in various applications outside the domain of astronomy. The objective of this study was to review and conduct a descriptive analysis of published studies that presented the importance of astronomy in the area of education. A narrative review of the literature has been performed, considering the articles published in the last five years. As astronomy involves the study of physics, chemistry, biology, mathematics and technology, one of the studies evaluated presented astronomy as the gateway to science, demonstrating the presence of astronomy in 52 school curricula in 37 countries, with celestial movement the dominant content area. Another intervention study, evaluating individuals aged 4-5 years, demonstrated that the attribution of personal characteristics to cosmic bodies, in addition to the use of comprehensive astronomy concepts, favored the learning of science in preschool-age children, considering the use of practical activities of accompaniment and free drawing. Aiming to measure scientific literacy, another study developed in Turkey, motivated the authorities of this country to change the teaching materials and curriculum of secondary schools after the term “astronomy” appeared as one of the most attractive subjects for young people aged 15 to 24. There are also reports in the literature of the use of pedagogical tools, such as the representation of the Solar System on a human scale, where students can walk along the orbits of the planets while studying the laws of dynamics. The use of this tool favored the teaching of the relationship between distance, duration and speed over the period of the planets, in addition to improving the motivation and well-being of students aged 14-16. An important impact of astronomy on education was demonstrated in the study that evaluated the participation of high school students in the Astronomical Olympiads and the International Astronomy Olympiad. The study concluded that these Olympics have considerable influence on students who pursue a career in teaching or research later on, many of whom are in the area of astronomy itself. In addition, the literature indicates that the teaching of astronomy in the digital age has facilitated the availability of data for researchers, but also for the general population. This fact can increase even more the curiosity that the astronomy area has always instilled in people and promote the dissemination of knowledge on an expanded scale. Currently, astronomy has been considered an important ally in strengthening the school curricula of children, adolescents and young adults. This has been used as teaching tools, in addition to being extremely useful for scientific literacy, being increasingly used in the area of education.

Keywords: astronomy, education area, teaching, review

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Authors: Uraib Sharaha, Guy Beck, Joseph Kapelushnik, Adam H. Agbaria, Itshak Lapidot, Shaul Mordechai, Ahmad Salman, Mahmoud Huleihel

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Infectious diseases cause a significant burden on the public health and the economic stability of societies all over the world for several centuries. A reliable detection of the causative agent of infection is not possible based on clinical features, since some of these infections have similar symptoms, including fever, sneezing, inflammation, vomiting, diarrhea, and fatigue. Moreover, physicians usually encounter difficulties in distinguishing between viral and bacterial infections based on symptoms. Therefore, there is an ongoing need for sensitive, specific, and rapid methods for identification of the etiology of the infection. This intricate issue perplex doctors and researchers since it has serious repercussions. In this study, we evaluated the potential of the mid-infrared spectroscopic method for rapid and reliable identification of bacterial and viral infections based on simple peripheral blood samples. Fourier transform infrared (FTIR) spectroscopy is considered a successful diagnostic method in the biological and medical fields. Many studies confirmed the great potential of the combination of FTIR spectroscopy and machine learning as a powerful diagnostic tool in medicine since it is a very sensitive method, which can detect and monitor the molecular and biochemical changes in biological samples. We believed that this method would play a major role in improving the health situation, raising the level of health in the community, and reducing the economic burdens in the health sector resulting from the indiscriminate use of antibiotics. We collected peripheral blood samples from young 364 patients, of which 93 were controls, 126 had bacterial infections, and 145 had viral infections, with ages lower than18 years old, limited to those who were diagnosed with fever-producing illness. Our preliminary results showed that it is possible to determine the infectious agent with high success rates of 82% for sensitivity and 80% for specificity, based on the WBC data.

Keywords: infectious diseases, (FTIR) spectroscopy, viral infections, bacterial infections.

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Authors: Salma A. Mahmoud

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Epigenetic, or alteration in gene expression influenced by extragenetic factors, has emerged as one of the most promising areas that will address some of the gaps in our current knowledge in understanding patterns of human variation. In the last decade, the research investigating epigenetic mechanisms in many fields has flourished and witnessed significant progress. It paved the way for a new era of integrated research especially between anthropology/archeology and life sciences. Skeletal remains are considered the most significant source of information for studying human variations across history, and by utilizing these valuable remains, we can interpret the past events, cultures and populations. In addition to archeological, historical and anthropological importance, studying bones has great implications in other fields such as medicine and science. Bones also can hold within them the secrets of the future as they can act as predictive tools for health, society characteristics and dietary requirements. Bones in their basic forms are composed of cells (osteocytes) that are affected by both genetic and environmental factors, which can only explain a small part of their variability. The primary objective of this project is to examine the epigenetic landscape/signature within bones of archeological remains as a novel marker that could reveal new ways to conceptualize chronological events, gender differences, social status and ecological variations. We attempted here to address discrepancies in common variants such as methylome as well as novel epigenetic regulators such as chromatin remodelers, which to our best knowledge have not yet been investigated by anthropologists/ paleoepigenetists using plethora of techniques (biological, computational, and statistical). Moreover, extracting epigenetic information from bones will highlight the importance of osseous material as a vector to study human beings in several contexts (social, cultural and environmental), and strengthen their essential role as model systems that can be used to investigate and construct various cultural, political and economic events. We also address all steps required to plan and conduct an epigenetic analysis from bone materials (modern and ancient) as well as discussing the key challenges facing researchers aiming to investigate this field. In conclusion, this project will serve as a primer for bioarcheologists/anthropologists and human biologists interested in incorporating epigenetic data into their research programs. Understanding the roles of epigenetic mechanisms in bone structure and function will be very helpful for a better comprehension of their biology and highlighting their essentiality as interdisciplinary vectors and a key material in archeological research.

Keywords: epigenetics, archeology, bones, chromatin, methylome

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Authors: Laribi-Habchi Hasiba, Bouanane-Darenfed Amel, Drouiche Nadjib, Pausse André, Mameri Nabil

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Chitin, a linear 1, 4-linked N-acetyl-d-glucosamine (GlcNAc) polysaccharide is the major structural component of fungal cell walls, insect exoskeletons and shells of crustaceans. It is one of the most abundant naturally occurring polysaccharides and has attracted tremendous attention in the fields of agriculture, pharmacology and biotechnology. Each year, a vast amount of chitin waste is released from the aquatic food industry, where crustaceans (prawn, crab, Shrimp and lobster) constitute one of the main agricultural products. This creates a serious environmental problem. This linear polymer can be hydrolyzed by bases, acids or enzymes such as chitinase. In this context an extracellular chitinase (ChiA-65) was produced and purified from a newly isolated LHH100. Pure protein was obtained after heat treatment and ammonium sulphate precipitation followed by Sephacryl S-200 chromatography. Based on matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis, the purified enzyme is a monomer with a molecular mass of 65,195.13 Da. The sequence of the 27 N-terminal residues of the mature ChiA-65 showed high homology with family-18 chitinases. Optimal activity was achieved at pH 4 and 75◦C. Among the inhibitors and metals tested p-chloromercuribenzoic acid, N-ethylmaleimide, Hg2+ and Hg + completelyinhibited enzyme activity. Chitinase activity was high on colloidal chitin, glycol chitin, glycol chitosane, chitotriose and chitooligosaccharide. Chitinase activity towards synthetic substrates in the order of p-NP-(GlcNAc) n (n = 2–4) was p-NP-(GlcNAc)2> p-NP-(GlcNAc)4> p-NP-(GlcNAc)3. Our results suggest that ChiA-65 preferentially hydrolyzed the second glycosidic link from the non-reducing end of (GlcNAc) n. ChiA-65 obeyed Michaelis Menten kinetics the Km and kcat values being 0.385 mg, colloidal chitin/ml and5000 s−1, respectively. ChiA-65 exhibited remarkable biochemical properties suggesting that this enzyme is suitable for bioconversion of chitin waste.

Keywords: Bacillus licheniformis LHH100, characterization, extracellular chitinase, purification

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Authors: Deybith Venegas-Rojas, Sercan Keskin, Svenja Riekeberg, Sana Azim, Stephanie Manz, R. J. Dwayne Miller, Hoc Khiem Trieu

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Liquid Transmission Electron Microscopy (TEM) is a growing area with a broad range of applications from physics and chemistry to material engineering and biology, in which it is possible to image in-situ unseen phenomena. For this, a nanofluidic device is used to insert the nanoflow with the sample inside the microscope in order to keep the liquid encapsulated because of the high vacuum. In the last years, Si3N4 windows have been widely used because of its mechanical stability and low imaging contrast. Nevertheless, the pressure difference between the inside fluid and the outside vacuum in the TEM generates bulging in the windows. This increases the imaged fluid volume, which decreases the signal to noise ratio (SNR), limiting the achievable spatial resolution. With the proposed device, the membrane is fortified with a microstructure capable of stand higher pressure differences, and almost removing completely the bulging. A theoretical study is presented with Finite Element Method (FEM) simulations which provide a deep understanding of the membrane mechanical conditions and proves the effectiveness of this novel concept. Bulging and von Mises Stress were studied for different membrane dimensions, geometries, materials, and thicknesses. The microfabrication of the device was made with a thin wafer coated with thin layers of SiO2 and Si3N4. After the lithography process, these layers were etched (reactive ion etching and buffered oxide etch (BOE) respectively). After that, the microstructure was etched (deep reactive ion etching). Then the back side SiO2 was etched (BOE) and the array of free-standing micro-windows was obtained. Additionally, a Pyrex wafer was patterned with windows, and inlets/outlets, and bonded (anodic bonding) to the Si side to facilitate the thin wafer handling. Later, a thin spacer is sputtered and patterned with microchannels and trenches to guide the nanoflow with the samples. This approach reduces considerably the common bulging problem of the window, improving the SNR, contrast and spatial resolution, increasing substantially the mechanical stability of the windows, allowing a larger viewing area. These developments lead to a wider range of applications of liquid TEM, expanding the spectrum of possible experiments in the field.

Keywords: liquid cell, liquid transmission electron microscopy, nanofluidics, nanofluidic cell, thin films

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Authors: Wael M. Rabeh, Cesar Carrasco-Lopez, Juliana C. Ferreira, Pance Naumov

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Bioluminescence, the emission of light from a biological process, is found in various living organisms including bacteria, fireflies, beetles, fungus and different marine organisms. Luciferase is an enzyme that catalyzes a two steps oxidation of luciferin in the presence of Mg2+ and ATP to produce oxyluciferin and releases energy in the form of light. The luciferase assay is used in biological research and clinical applications for in vivo imaging, cell proliferation, and protein folding and secretion analysis. The luciferase enzyme consists of two domains, a large N-terminal domain (1-436 residues) that is connected to a small C-terminal domain (440-544) by a flexible loop that functions as a hinge for opening and closing the active site. The two domains are separated by a large cleft housing the active site that closes after binding the substrates, luciferin and ATP. Even though all insect luciferases catalyze the same chemical reaction and share 50% to 90% sequence homology and high structural similarity, they emit light of different colors from green at 560nm to red at 640 nm. Currently, the majority of the structural and biochemical studies have been conducted on green-emitting firefly luciferases. To address the color emission mechanism, we expressed and purified two luciferase enzymes with blue-shifted green and red emission from indigenous Brazilian species Amydetes fanestratus and Phrixothrix, respectively. The two enzymes naturally emit light of different colors and they are an excellent system to study the color-emission mechanism of luciferases, as the current proposed mechanisms are based on mutagenesis studies. Using a vapor-diffusion method and a high-throughput approach, we crystallized and solved the crystal structure of both enzymes, at 1.7 Å and 3.1 Å resolution respectively, using X-ray crystallography. The free enzyme adopted two open conformations in the crystallographic unit cell that are different from the previously characterized firefly luciferase. The blue-shifted green luciferase crystalized as a monomer similar to other luciferases reported in literature, while the red luciferases crystalized as an octamer and was also purified as an octomer in solution. The octomer conformation is the first of its kind for any insect’s luciferase, which might be relate to the red color emission. Structurally designed mutations confirmed the importance of the transition between the open and close conformations in the fine-tuning of the color and the characterization of other interesting mutants is underway.

Keywords: bioluminescence, enzymology, structural biology, x-ray crystallography

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Authors: A. Aslihan Gokaltun, Martin L. Yarmush, Ayse Asatekin, O. Berk Usta

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Poly(dimethylsiloxane) (PDMS) is one of the most widely used materials in the fabrication of microfluidic devices. It is easily patterned and can replicate features down to nanometers. Its flexibility, gas permeability that allows oxygenation, and low cost also drive its wide adoption. However, a major drawback of PDMS is its hydrophobicity and fast hydrophobic recovery after surface hydrophilization. This results in significant non-specific adsorption of proteins as well as small hydrophobic molecules such as therapeutic drugs limiting the utility of PDMS in biomedical microfluidic circuitry. While silicon, glass, and thermoplastics have been used, they come with problems of their own such as rigidity, high cost, and special tooling needs, which limit their use to a smaller user base. Many strategies to alleviate these common problems with PDMS are lack of general practical applicability, or have limited shelf lives in terms of the modifications they achieve. This restricts large scale implementation and adoption by industrial and research communities. Accordingly, we aim to tailor biocompatible PDMS surfaces by developing a simple and one step bulk modification approach with novel smart materials to reduce non-specific molecular adsorption and to stabilize long-term cell analysis with PDMS substrates. Smart polymers that blended with PDMS during device manufacture, spontaneously segregate to surfaces when in contact with aqueous solutions and create a < 1 nm layer that reduces non-specific adsorption of organic and biomolecules. Our methods are fully compatible with existing PDMS device manufacture protocols without any additional processing steps. We have demonstrated that our modified PDMS microfluidic system is effective at blocking the adsorption of proteins while retaining the viability of primary rat hepatocytes and preserving the biocompatibility, oxygen permeability, and transparency of the material. We expect this work will enable the development of fouling-resistant biomedical materials from microfluidics to hospital surfaces and tubing.

Keywords: cell culture, microfluidics, non-specific protein adsorption, PDMS, smart polymers

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Authors: Zeina Bourhane, Anders Lanzen, Christine Cagnon, Olfa Ben Said, Cristiana Cravo-Laureau, Robert Duran

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The anthropogenic pressure in coastal areas increases dramatically with the exploitation of environmental resources. Biomonitoring coastal areas are crucial to determine the impact of pollutants on bacterial communities in soils and sediments since they provide important ecosystem services. However, relevant biomonitoring tools allowing fast determination of the ecological status are yet to be defined. Microbial ecology approaches provide useful information for developing such microbial monitoring tools reporting on the effect of environmental stressors. Chemical and microbial molecular approaches were combined in order to determine microbial bioindicators for assessing the ecological status of soil and river ecosystems around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected along soil/river/lake continuums in three stations around the Ichkeul Lake influenced by different human activities at two seasons (summer and winter). Contaminant pressure indexes (PI), including PAHs (Polycyclic aromatic hydrocarbons), alkanes, and OCPs (Organochlorine pesticides) contents, showed significant differences in the contamination level between the stations with seasonal variation. Bacterial communities were characterized by 16S ribosomal RNAs (rRNA) gene metabarcoding. Although microgAMBI indexes, determined from the sequencing data, were in accordance with contaminant contents, they were not sufficient to fully explain the PI. Therefore, further microbial indicators are still to be defined. The comparison of bacterial communities revealed the specific microbial assemblage for soil, river, and lake sediments, which were significantly correlated with contaminant contents and PI. Such observation offers the possibility to define a relevant set of bioindicators for reporting the effects of human activities on the microbial community structure. Such bioindicators might constitute useful monitoring tools for the management of microbial communities in coastal areas.

Keywords: bacterial communities, biomonitoring, contamination, human impacts, microbial bioindicators

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Authors: Andrea Giacomelli, Luciano Massetti, Elena Maggi, Antonio Raschi

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The presentation will report the activities managed during the Summer of 2017 by a team composed by staff from a University Department, a National Research Council Institute, and an outreach NGO, collecting measurements of night sky brightness and other information on artificial lighting, in order to characterize light pollution issues on portions of the Tuscan coast, in Central Italy. These activities combine measurements collected by the principal scientists, citizen science observations led by students, and outreach events targeting a broad audience. This campaign aggregates the efforts of three actors: the BuioMetria Partecipativa project, which started collecting light pollution data on a national scale in 2008 with an environmental engineering and free/open source GIS core team; the Institute of Biometeorology from the National Research Council, with ongoing studies on light and urban vegetation and a consolidated track record in environmental education and citizen science; the Department of Biology from the University of Pisa, which started experiments to assess the impact of light pollution in coastal environments in 2015. While the core of the activities concerns in situ data, the campaign will account also for remote sensing data, thus considering heterogeneous data sources. The aim of the campaign is twofold: (1) To test actions of citizen and student engagement in monitoring sky brightness (2) To collect night sky brightness data and test a protocol for applications to studies on the ecological impact of light pollution, with a special focus on marine coastal ecosystems. The collaboration of an interdisciplinary team in the study of artificial lighting issues is not a common case in Italy, and the possibility of undertaking the campaign in Tuscany has the added value of operating in one of the territories where it is possible to observe both sites with extremely high lighting levels, and areas with extremely low light pollution, especially in the Southern part of the region. Combining environmental monitoring and communication actions in the context of the campaign, this effort will contribute to the promotion of night skies with a good quality as an important asset for the sustainability of coastal ecosystems, as well as to increase citizen awareness through star gazing, night photography and actively participating in field campaign measurements.

Keywords: citizen science, light pollution, marine coastal biodiversity, environmental education

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Authors: Fang Liu, JunShuai Xue, JiaJia Yao, GuanLin Wu, ZuMaoLi, XueYan Yang, HePeng Zhang, ZhiPeng Sun

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Terahertz spectra is in great demand since last two decades for many photonic and electronic applications. III-Nitride resonant tunneling diode is one of the promising candidates for portable and compact THz sources. Room temperature microwave oscillator based on GaN/AlN resonant tunneling diode was reported in this work. The devices, grown by plasma-assisted molecular-beam epitaxy on free-standing c-plane GaN substrates, exhibit highly repeatable and robust negative differential resistance (NDR) characteristics at room temperature. To improve the interface quality at the active region in RTD, indium surfactant assisted growth is adopted to enhance the surface mobility of metal atoms on growing film front. Thanks to the lowered valley current associated with the suppression of threading dislocation scattering on low dislocation GaN substrate, a positive peak current density of record-high 2.1 MA/cm2 in conjunction with a peak-to-valley current ratio (PVCR) of 1.2 are obtained, which is the best results reported in nitride-based RTDs up to now considering the peak current density and PVCR values simultaneously. When biased within the NDR region, microwave oscillations are measured with a fundamental frequency of 0.31 GHz, yielding an output power of 5.37 µW. Impedance mismatch results in the limited output power and oscillation frequency described above. The actual measured intrinsic capacitance is only 30fF. Using a small-signal equivalent circuit model, the maximum intrinsic frequency of oscillation for these diodes is estimated to be ~260GHz. This work demonstrates a microwave oscillator based on resonant tunneling effect, which can meet the demands of terahertz spectral devices, more importantly providing guidance for the fabrication of the complex nitride terahertz and quantum effect devices.

Keywords: GaN resonant tunneling diode, peak current density, microwave oscillation, intrinsic capacitance

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Authors: Harika Atmaca, Emir Bozkurt, Latife Merve Oktay, Selim Uzunoglu, Ruchan Uslu, Burçak Karaca

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Microarrays have been developed for highly parallel enzyme-linked immunosorbent assay (ELISA) applications. The most common protein arrays are produced by using multiple monoclonal antibodies, since they are robust molecules which can be easily handled and immobilized by standard procedures without loss of activity. Protein expression profiling with protein array technology allows simultaneous analysis of the protein expression pattern of a large number of proteins. Trabectedin, a tetrahydroisoquinoline alkaloid derived from a Caribbean tunicate, Ecteinascidia turbinata, has been shown to have antitumor effects. Here, we used a novel proteomic approach to explore the mechanism of action of trabectedin in prostate cancer cell line PC-3 by apoptosis antibody microarray. XTT cell proliferation kit and Cell Death Detection Elisa Plus Kit (Roche) was used for measuring cytotoxicity and apoptosis. Human Apoptosis Protein Array (R&D Systems) which consists of 35 apoptosis related proteins was used to assess the omic protein expression pattern. Trabectedin induced cytotoxicity and apoptosis in prostate cancer cells in a time and concentration-dependent manner. The expression levels of the death receptor pathway molecules, TRAIL-R1/DR4, TRAIL R2/DR5, TNF R1/TNFRSF1A, FADD were significantly increased by 4.0-, 21.0-, 4.20- and 11.5-fold by trabectedin treatment in PC-3 cells. Moreover, mitochondrial pathway related pro-apoptotic proteins Bax, Bad, Cytochrome c, and Cleaved Caspase-3 expressions were induced by 2.68-, 2.07-, 2.8-, and 4.5-fold and the expression levels of anti-apoptotic proteins Bcl-2 and Bcl-XL were reduced by 3.5- and 5.2-fold in PC-3 cells. Proteomic (antibody microarray) analysis suggests that the mechanism of action of trabectedin may be exerted via the induction of both intrinsic and extrinsic apoptotic pathways. The antibody microarray platform can be utilised to explore the molecular mechanism of action of novel anticancer agents.

Keywords: trabectedin, prostate cancer, omic protein expression profile, apoptosis

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Authors: A. Gilewska, J. Masternak, K. Kazimierczuk, L. Turlej, J. Wietrzyk, B. Barszcz

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Platinum-based drugs are now widely used as chemotherapeutic agents. However the platinum complexes show the toxic side-effects: i) the development of platinum resistance; ii) the occurrence of severe side effects, such as nephro-, neuro- and ototoxicity; iii) the high toxicity towards human fibroblast. Therefore the development of new anticancer drugs containing different transition-metal ions, for example, ruthenium, rhodium, iridium is a valid strategy in cancer treatment. In this paper, we reported the synthesis, spectroscopic, structural and biological properties of complexes of ruthenium, rhodium, and iridium containing N,N-chelating ligand (2,2’-bisimidazole). These complexes were characterized by elemental analysis, UV-Vis and IR spectroscopy, X-ray diffraction analysis. These complexes exhibit a typical pseudotetrahedral three-legged piano-stool geometry, in which the aromatic arene ring forms the seat of the piano-stool, while the bidentate 2,2’-bisimidazole (ligand) and the one chlorido ligand form the three legs of the stool. The spectroscopy data (IR, UV-Vis) and elemental analysis correlate very well with molecular structures. Moreover, the cytotoxic activity of the complexes was carried out on human cancer cell lines: LoVo (colorectal adenoma), MV-4-11 (myelomonocytic leukaemia), MCF-7 (breast adenocarcinoma) and normal healthy mouse fibroblast BALB/3T3 cell lines. To predict a binding mode, a potential interaction of metal complexes with calf thymus DNA (CT-DNA) and protein (BSA) has been explored using UV absorption and circular dichroism (CD). It is interesting to note that the investigated complexes show no cytotoxic effect towards the normal BALB/3T3 cell line, compared to cisplatin, which IC₅₀ values was determined as 2.20 µM. Importantly, Ru(II) displayed the highest activity against HL-60 (IC₅₀ 4.35 µM). The biological studies (UV-Vis and circular dichroism) suggest that arene-complexes could interact with calf thymus DNA probably via an outside binding mode and interact with protein (BSA).

Keywords: ruthenium(II) complex, rhodium(III) complex, iridium(III) complex, biological activity

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Authors: Young Ah Kim, Hyunsoo Kim, Eun-Jeong Yoon, Young Hee Seo, Kyungwon Lee

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from food animals are considered as a reservoir for transmission of ESBL genes to human. The aim of this study is to assess the prevalence and molecular epidemiology of ESBL-producing E. coli colonization in pigs, farm workers, and farm environments to elucidate the transmission of multidrug-resistant clones from animal to human. Nineteen pig farms were enrolled across the country in Korea from August to December 2017. ESBL-producing E. coli isolates were detected in 190 pigs, 38 farm workers, and 112 sites of farm environments using ChromID ESBL (bioMerieux, Marcy l'Etoile, France), directly (stool or perirectal swab) or after enrichment (sewage). Antimicrobial susceptibility tests were done with disk diffusion methods and blaTEM, blaSHV, and blaCTX-M were detected with PCR and sequencing. The genomes of the four CTX-M-55-producing E. coli isolates from various sources in one farm were entirely sequenced to assess the relatedness of the strains. Whole genome sequencing (WGS) was performed with PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA). ESBL genotypes were 85 CTX-M-1 group (one CTX-M-3, 23 CTX-M-15, one CTX-M-28, 59 CTX-M-55, one CTX-M-69) and 60 CTX-M-9 group (41 CTX-M-14, one CTX-M-17, one CTX-M-27, 13 CTX-M-65, 4 CTX-M-102) in total 145 isolates. The rectal colonization rates were 53.2% (101/190) in pigs and 39.5% (15/38) in farm workers. In WGS, sequence types (STs) were determined as ST69 (E. coli PJFH115 isolate from a human carrier), ST457 (two E. coli isolates PJFE101 recovered from a fence and PJFA1104 from a pig) and ST5899 (E. coli PJFA173 isolate from the other pig). The four plasmids encoding CTX-M-55 (88,456 to 149, 674 base pair), whether it belonged to IncFIB or IncFIC-IncFIB type, shared IncF backbone furnishing the conjugal elements, suggesting of genes originated from same ancestor. In conclusion, the prevalence of ESBL-producing E. coli in swine farms was surprisingly high, and many of them shared common ESBL genotypes of clinical isolates such as CTX-M-14, 15, and 55 in Korea. It could spread by horizontal transfer between isolates from different reservoirs (human-animal-environment).

Keywords: Escherichia coli, extended-spectrum β-lactamase, prevalence, whole genome sequencing

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Islam Nowisser, Noha Farag, Mohamed El Azizi

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Helicobacter pylori is a highly important human pathogen which inhabits about 50% of the population worldwide. Infection with this bacteria is very hard to treat, with high probability of recurrence. H. pylori causes severe gastric diseases, including peptic ulcer, gastritis, and gastric cancer, which has been linked to chronic inflammation. The infection has been reported to be associated with high levels of pro-inflammatory cytokines, especially IL-1β and TNF-α. The aim of the current study is to investigate the molecular mechanisms by which H. pylori activates NLRP3 inflammasome and its contribution to Il-1 β production in an innate cellular model. H. pylori PMSS1 and G27 standard strains, as well as the PMSS1 isogenic mutant strain PMSS1ΔVacA and G27ΔVacA, G27ΔCagA in addition to clinical isolates obtained from biopsy samples from the antrum and corpus mucosa of chronic gastritis patients, were used to establish infection in RAW-264.7 macrophages. The production levels of TNF-α and IL-1β was assessed using ELISA. Since expression of these cytokines is often regulated by the transcription factor complex, nuclear factor-kB (NF-kB), the activation of NF-κB in H. pylori infected cells was also evaluated by luciferase assay. Genomic DNA was extracted from bacterial cultures of H. pylori clinical isolates as well as the standard strains and their corresponding mutants, where they were evaluated for the cagA pathogenicity island and vacA expression. The correlation between these findings and expression of the cagA Pathogenicity Island and vacA in the bacteria was also investigated. The results showed IL-1β, and TNF-α production significantly increased in raw macrophages following H. pylori infection. The cagA+ and vacA+ H. pylori strains induced significant production of IL-1β compared to cagA- and vacA- strains. The activation pattern of NF-κB was correlated in the isolates to their cagA and vacA expression profiles. A similar finding could not be confirmed for TNF-α production. Our study shows the ability of H. pylori to activate NF-kB and induce significant IL-1β production as a possible mechanism for the augmented inflammatory response seen in subjects infected with cagA+ and vacA+ H. pylori strains that would lead to the progression to more severe form of the disease.

Keywords: Helicobacter pylori, IL-1β, inflammatory cytokines, nuclear factor KB, TNF-α

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Authors: Sudhakara Naidu Neppalli, Tejas S. Bhosale

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It is well known that the block copolymer (BCP) can form a complex molecule, through non-covalent bonds such as hydrogen bond, ionic bond and co-ordination bond, with low molecular weight compound as well as with macromolecules, which provide vast applications, includes the alteration of morphology and properties of polymers. Hence we covered the research that, the importance of non-covalent bonds in increasing the non-favourable segmental interactions of the blocks was well examined by attaching and detaching the bonds between the BCP and additive. We also monitored the phase transition of block copolymer and effective interaction parameter (χeff) for Li-doped polymers using small angle x-ray scattering and transmission electron microscopy. The effective interaction parameter (χeff) between two block components was evaluated using Leibler theory based on the incompressible random phase approximation (RPA) for ionized BCP in a disordered state. Furthermore, conductivity experiments demonstrate that the ionic conductivity in the samples quenched from the different structures is morphology-independent, while it increases with increasing ion salt concentration. Morphological transitions, interaction parameter, and thermal stability also examined in quarternized block copolymer. D-spacing was used to estimate effective interaction parameter (χeff) of block components in weak and strong segregation regimes of ordered phase. Metal-containing polymer has been the topic of great attention in recent years due to their wide range of potential application. Similarly, metal- ligand complex is used as a supramolecular linker between the polymers giving rise to a ‘Metallo-Supramolecule assembly. More precisely, functionalized polymer end capped with 2, 2’:6’, 2”- terpyridine ligand can be selectively complexed with wide range of transition metal ions and then subsequently attached to other terpyridine terminated polymer block. In compare to other supramolecular assembly, BCP involved metallo-supramolecule assembly offers vast applications such as optical activity, electrical conductivity, luminescence and photo refractivity.

Keywords: band gap, block copolymer, conductivity, interaction parameter, phase transition

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Authors: Yassir Adam Shuaib, Stefan Niemann, Eltahir Awad Khalil, Ulrich Schaible, Lothar Heinz Wieler, Mohammed Ahmed Bakhiet, Abbashar Osman Mohammed, Mohamed Abdelsalam Abdalla, Elvira Richter

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Tuberculosis (TB) is a chronic bacterial disease of humans and animals and it is characterized by the progressive development of specific granulomatous tubercle lesions in affected tissues. In a six-month study, from June to November 2014, a total of 2,304 carcasses of cattle, camel, sheep, and goats slaughtered at East and West Gaash slaughterhouses, Kassala, were investigated during postmortem, in parallel, 101 sputum samples from TB suspected patients at Kassala and El-Gadarif Teaching Hospitals were collected in order to investigate tuberculosis in animals and humans. Only 0.1% carcasses were found with suspected TB lesions in the liver and lung and peritoneal cavity of two sheep and no tuberculous lesions were found in the carcasses of cattle, goats or camels. All samples, tissue lesions and sputum, were decontaminated by the NALC-NaOH method and cultured for mycobacterial growth at the NRZ for Mycobacteria, Research Center Borstel, Germany. Genotyping and molecular characterization of the grown strains were done by line probe assay (GenoType CM and MTBC) and 16S rDNA, rpoB gene, and ITS sequencing, spoligotyping, MIRU-VNTR typing and next generation sequencing (NGS). Culture of the specimens revealed growth of organisms from 81.6% of all samples. Mycobacterium tuberculosis (76.2%), M. intracellulare (14.2%), mixed infection with M. tuberculosis and M. intracellulare (6.0%) and mixed infection with M. tuberculosis and M. fortuitum and with M. intracellulare and unknown species (1.2%) were detected in the sputum samples and unknown species (1.2%) were detected in the samples of one of the animals tissues. From the 69 M. tuberculosis strains, 25 (36.2%) were showing either mono-drug-resistant or multi-drug-resistant or poly-drug-resistant but none was extensively drug-resistant. In conclusion, the prevalence of TB in animals was very low while in humans M. tuberculosis-Delhi/CAS lineage was responsible for most cases and there was an evidence of MDR transmission and acquisition.

Keywords: animal, human, slaughterhouse, Sudan, tuberculosis

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