Search results for: sequencing batch reactor

Authors: Mohammadreza Hajialigol, Nargues Falahi Charkhabi, Fatemeh Shahryari, Saadat Sarikhani

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BACKGROUND AND OBJECTIVES Walnut canker is characterized by brown to blackish roundish blotches on the trunks and main branches, necrosis of inner bark and bleeding with dark brown to black-colored exudates. The present study aimed to identify the causative agents of walnut decline by their phenotypic features, approval of pathogenicity, the partial sequencing of the housekeeping genes in Razavi Khorasan. MATERIAL AND METHODS Ten Symptomatic samples were collected from walnut orchards of Razavi Khorasan in 2019. Pathogenicity of all isolated strains was carried out on walnut immature fruits cv. ‘Hartley’ and young green twigs of cv. ‘Chandler’. All pathogenic strains were subjected to physiological, morphological and biochemical tests. 16S rRNA and housekeeping genes (fusA, leuS, and pyrG) were partially amplified and sequenced. RESULTS Eight strains were able to cause necrosis and a dark-colored region in the mesocarp of immature walnut fruits, and three representative strains caused necrosis on young inoculated twigs. Strains utilized starch, however, did not utilized esculin, Tween 20, Tween 80, and gelatin. The partial 16S rRNA gene sequence of strain KH7 indicated 99.63 % similarity to that of Citrobacter braakii ATCC5113T. The phylogenetic analyses based on the partial sequencing of three housekeeping genes, fusA (633 bp), pyrG (305), and leuS (640 bp), demonstrated that strains KH1, KH3, and KH7 belong to C. braakii species in a monophyletic clade with high bootstrap support. CONCLUSION To the best of our knowledge, this is the first report of C. braakii as a new plant pathogen which cause walnut decline. Identification of bacteria associated with walnut decline will eventually improve our understanding of the etiology of the disease and may result in improved management techniques for control.

Keywords: emerging pathogens, Iran, juglans regia, MLSA

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

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Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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Authors: D. Nkazi, S. E. Iyuke, J. Mulopo

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Increasing global energy demand as well as air quality concerns have in recent years led to the search for alternative clean fuels to replace fossil fuels. One such alternative is the blending of petrol with ethanol, which has numerous advantages such ethanol’s ability to act as oxygenate thus reducing the carbon monoxide emissions from the exhaust of internal combustion engines of vehicles. However, the hygroscopic nature of ethanol is a major concern in obtaining a perfectly homogenized petrol-ethanol fuel. This problem has led to the study of ways of homogenizing the petrol-ethanol mixtures. During the blending process, volumes fraction of ethanol and petrol were studied with respect to the depth within the storage container to confirm homogenization of the blend and time of storage. The results reveal that the density of the mixture was constant. The binodal curve of the ternary diagram shows an increase of homogeneous region, indicating an improved of interaction between water and petrol. The concentration distribution in the reactor showed proof of cavitation formation since in both directions, the variation of concentration with both time and distance was found to be oscillatory. On comparing the profiles in both directions, the concentration gradient, diffusion flux, and energy and diffusion rates were found to be higher in the vertical direction compared to the horizontal direction. It was therefore concluded that ultrasonication creates cavitation in the mixture which enhances mass transfer and mixing of ethanol and petrol. The horizontal direction was found to be the diffusion rate limiting step which proposed that the blender should have a larger height to diameter ratio. It is, however, recommended that further studies be done on the rate-limiting step so as to have actual dimensions of the reactor.

Keywords: ultrasonication, petrol, ethanol, concentration

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: Dwi Arisandi Wijaya, Ernawati Arifin Giri-Rachman, Neni Nurainy

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Typhoid fever disease can be prevented by using a polysaccharide-based vaccine Vi which is a virulence factor of S.typhi. To produce high yield Vi polysaccharide from bacteria, it is important to know the biosynthesis of Vi polysaccharide and the regulators involved. In the In vivo condition, S. typhi faces different osmolarity, and the bacterial two-component system OmpR-EnvZ, regulate by up and down Capsular Vi polysaccharide biosynthesis. A high yielded Vi Polysaccharide strain, S. typhi strain C6524 used to study the effect of media osmolarity on Vi polysaccharide biosynthesis and the osmoregulation pattern of S. typhi strain C6524. The methods were performed by grown S. typhi strain C6524 grown on medium with 50 mM, 100 mM, and 150 mM osmolarity with the batch system. Vi polysaccharide concentration was measured by ELISA method. For further investigation of the osmoregulation pattern of strain C6524, the osmoregulator gene, OmpR, has been isolated and sequenced using the specific primer of the OmpR gene. Nucleotide sequence analysis is done with BLAST and Lallign. Amino Acid sequence analysis is done with Prosite and Multiple Sequence Alignment. The results of cultivation showed the average content of polysaccharide Vi for 50 mM, 100 mM, and 150 mM osmolarities 11.49 μg/mL, 12.06 μg/mL, and 14.53 μg/mL respectively. Analysis using Anova stated that the osmolarity treatment of 150 mM significantly affects Vi content. Analysis of nucleotide sequences shows 100% identity between S. typhi strain C6524 and Ty2. Analysis of amino acid sequences shows that the OmpR response regulator protein of the C6524 strain also has a α4-β5-α5 motif which is important for the regulatory activation system when phosphorylation occurs by domain kinase. This indicates that the regulator osmolarity response of S. typhi strain C6524 has no difference with the response regulator owned by S. typhi strain Ty2. A high Vi response rate in the 150 mM osmolarity treatment requires further research for RcsB-RcsC, another two-component system involved in Vi Biosynthesis.

Keywords: osmoregulator, OmpR, Salmonella, Vi polysaccharide

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Authors: Supriya Ambawat, Subaran Singh, C. Tara Satyavathi, B. S. Rajpurohit, Ummed Singh, Balraj Singh

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Pearl millet [Pennisetum glaucum (L.) R. Br.] is an important staple food of the arid and semiarid tropical regions of Asia, Africa, and Latin America. It is rightly termed as nutricereal as it has high nutrition value and a good source of carbohydrate, protein, fat, ash, dietary fiber, potassium, magnesium, iron, zinc, etc. Pearl millet has low prolamine fraction and is gluten free which is useful for people having a gluten allergy. It has several health benefits like reduction in blood pressure, thyroid, diabe¬tes, cardiovascular and celiac diseases but its direct consumption as food has significantly declined due to several reasons. Keeping this in view, it is important to reorient the ef¬forts to generate demand through value-addition and quality improvement and create awareness on the nutritional merits of pearl millet. In India, through Indian Council of Agricultural Research-All India Coordinated Research Project on Pearl millet, multilocational coordinated trials for developed hybrids were conducted at various centers. The gene banks of pearl millet contain varieties with high levels of iron and zinc which were used to produce new pearl millet varieties with elevated iron levels bred with the high‐yielding varieties. Thus, using breeding approaches and biochemical analysis, a total of 167 hybrids and 61 varieties were identified and released for cultivation in different agro-ecological zones of the country which also includes some biofortified hybrids rich in Fe and Zn. Further, using several biotechnological interventions such as molecular markers, next-generation sequencing (NGS), association mapping, nested association mapping (NAM), MAGIC populations, genome editing, genotyping by sequencing (GBS), genome wide association studies (GWAS) advancement in millet improvement has become possible by identifying and tagging of genes underlying a trait in the genome. Using DArT markers very high density linkage maps were constructed for pearl millet. Improved HHB67 has been released using marker assisted selection (MAS) strategies, and genomic tools were used to identify Fe-Zn Quantitative Trait Loci (QTL). The draft genome sequence of millet has also opened various ways to explore pearl millet. Further, genomic positions of significantly associated simple sequence repeat (SSR) markers with iron and zinc content in the consensus map is being identified and research is in progress towards mapping QTLs for flour rancidity. The sequence information is being used to explore genes and enzymatic pathways responsible for rancidity of flour. Thus, development and application of several biotechnological approaches along with biofortification can accelerate the genetic gain targets for pearl millet improvement and help improve its quality.

Keywords: Biotechnological approaches, genomic tools, malnutrition, MAS, nutricereal, pearl millet, sequencing.

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Authors: Amriana Hifizah, Philip Edward Vercoe, Graeme Bruce Martin, Teuku Reza Ferasy, Muhammad Hambal

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Many native forage plant species have been used in Indonesia as feed for ruminants. However, less information is available about how these plants affect productivity, let alone methane emissions. In the province of Aceh, where the traditional practice is to feed local forages to small ruminants, the farmers are not satisfied with the productivity of their livestock, and they attribute this problem to poor availability and too few options for good quality forages. Forage quality is reduced by high environmental temperatures which increase the amount of lignification. In addition to reducing productivity, these factors also increase enteric methane production. A preliminary survey about potential forage species was completed in three different districts, two of low elevation and one of high elevation: Syiah Kuala (05°30’5.08” N to 095°24’7.35” E), elevation 29 m MSL; Kajhu (05°32’34.6” N to 095°21’17.7” E), elevation 30 m MSL; Lembah Seulawah (05°28'06.4" N to 095°43' 14.2" E), elevation 254 m MSL. Information about local plants was collected in a semi-structured interview with scientists, government field officers and local farmers, in the city of Banda Aceh and in those three districts. The outcome was a list 40 species that could be useful, of which 21 were selected for further study. The selection process was based on several criteria: high availability, high protein content, low toxicity, and evidence of secondary metabolites (eg, history of medicinal plants for both human and animals). For some of the selected medicinal plants, there is experimental evidence of effects on methane production during rumen fermentation. Subsequently, the selected forages were tested for their effects on rumen fermentation in vitro, using batch culture. The data produced will be used to identify forages with the potential to reduce CH4 emissions. These candidates will then be assessed for their benefits (fermentability and productivity) and potential deleterious side-effects.

Keywords: batch culture, forage, methane, rumen

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Authors: Miguel A. Figueroa, José A. Lara-Ramos, Miguel A. Mueses

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Pharmaceutical residues are a section of emerging contaminants of anthropogenic origin that are present in a myriad of waters with which human beings interact daily and are starting to affect the ecosystem directly. Conventional waste-water treatment systems are not capable of degrading these pharmaceutical effluents because their designs cannot handle the intermediate products and biological effects occurring during its treatment. That is why it is necessary to hybridize conventional waste-water systems with non-conventional processes. In the specific case of an ozonation process, its efficiency highly depends on a perfect dispersion of ozone, long times of interaction of the gas-liquid phases and the size of the ozone bubbles formed through-out the reaction system. In order to increase the efficiency of these parameters, the use of a modified flotation cell has been proposed recently as a reactive system, which is used at an industrial level to facilitate the suspension of particles and spreading gas bubbles through the reactor volume at a high rate. The objective of the present work is the development of a mathematical model that can closely predict the kinetic rates of reactions taking place in the flotation cell at an experimental scale by means of identifying proper reaction mechanisms that take into account the modified chemical and hydrodynamic factors in the FeO-catalyzed Ozonation of Diclofenac aqueous solutions in a flotation cell. The methodology is comprised of three steps: an experimental phase where a modified flotation cell reactor is used to analyze the effects of ozone concentration and loading catalyst over the degradation of Diclofenac aqueous solutions. The performance is evaluated through an index of utilized ozone, which relates the amount of ozone supplied to the system per milligram of degraded pollutant. Next, a theoretical phase where the reaction mechanisms taking place during the experiments must be identified and proposed that details the multiple direct and indirect reactions the system goes through. Finally, a kinetic model is obtained that can mathematically represent the reaction mechanisms with adjustable parameters that can be fitted to the experimental results and give the model a proper physical meaning. The expected results are a robust reaction rate law that can simulate the improved results of Diclofenac mineralization on water using the modified flotation cell reactor. By means of this methodology, the following results were obtained: A robust reaction pathways mechanism showcasing the intermediates, free-radicals and products of the reaction, Optimal values of reaction rate constants that simulated Hatta numbers lower than 3 for the system modeled, degradation percentages of 100%, TOC (Total organic carbon) removal percentage of 69.9 only requiring an optimal value of FeO catalyst of 0.3 g/L. These results showed that a flotation cell could be used as a reactor in ozonation, catalytic ozonation and photocatalytic ozonation processes, since it produces high reaction rate constants and reduces mass transfer limitations (Ha > 3) by producing microbubbles and maintaining a good catalyst distribution.

Keywords: advanced oxidation technologies, iron oxide, emergent contaminants, AOTS intensification

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Authors: Vincent Murray

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The chromatin structure at the transcription start sites (TSSs) of genes is very important in the control of gene expression. In order for gene expression to occur, the chromatin structure at the TSS has to be altered so that the transcriptional machinery can be assembled and RNA transcripts can be produced. In particular, the nucleosome structure and positioning around the TSS has to be changed. Bleomycin is utilized as an anti-tumor agent to treat Hodgkin's lymphoma, squamous cell carcinoma, and testicular cancer. Bleomycin produces DNA damage in human cells and DNA strand breaks, especially double-strand breaks, are thought to be responsible for the cancer chemotherapeutic activity of bleomycin. Bleomycin is a large glycopeptide with molecular weight of approximately 1500 Daltons and hence its DNA strand cleavage activity can be utilized as a probe of chromatin structure. In this project, Illumina next-generation DNA sequencing technology was used to determine the position of DNA double-strand breaks at the TSSs of genes in intact cells. In this genome-wide study, it was found that bleomycin cleavage preferentially occurred at the TSSs of actively transcribed human genes in comparison with non-transcribed genes. There was a correlation between the level of enhanced bleomycin cleavage at TSSs and the degree of transcriptional activity. In addition, bleomycin was able to determine the position of nucleosomes at the TSSs of human genes. Bleomycin analogues were also utilized as probes of chromatin structure at the TSSs of human genes. In a similar manner to bleomycin, the bleomycin analogues 6′-deoxy-BLM Z and zorbamycin preferentially cleaved at the TSSs of human genes. Interestingly this degree of enhanced TSS cleavage inversely correlated with the cytotoxicity (IC50 values) of BLM analogues. This indicated that the degree of cleavage by bleomycin analogues at the TSSs of human genes was very important in the cytotoxicity of bleomycin and analogues. It also provided a deeper insight into the mechanism of action of this cancer chemotherapeutic agent since actively transcribed genes were preferentially targeted.

Keywords: anti-cancer activity, chromatin structure, cytotoxicity, gene expression, next-generation DNA sequencing

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Authors: S. Agarwal, A. Rani

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Catechol is a natural polyphenolic compound that widely exists in higher plants such as teas, vegetables, fruits, tobaccos, and some traditional Chinese medicines. The fly ash-based zeolites are capable of absorbing a wide range of pollutants. But the process of zeolite synthesis is time-consuming and requires technical setups by the industries. The marketed costs of zeolites are quite high restricting its use by small-scale industries for the removal of phenolic compounds. The present research proposes a simple method of alkaline treatment of FA to produce an effective adsorbent for catechol removal from wastewater. The experimental parameter such as pH, temperature, initial concentration and adsorbent dose on the removal of catechol were studied in batch reactor. For this purpose the adsorbent materials were mixed with aqueous solutions containing catechol ranging in 50 – 200 mg/L initial concentrations and then shaken continuously in a thermostatic Orbital Incubator Shaker at 30 ± 0.1 °C for 24 h. The samples were withdrawn from the shaker at predetermined time interval and separated by centrifugation (Centrifuge machine MBL-20) at 2000 rpm for 4 min. to yield a clear supernatant for analysis of the equilibrium concentrations of the solutes. The concentrations were measured with Double Beam UV/Visible spectrophotometer (model Spectrscan UV 2600/02) at the wavelength of 275 nm for catechol. In the present study, the use of low-cost adsorbent (BTFA) derived from coal fly ash (FA), has been investigated as a substitute of expensive methods for the sequestration of catechol. The FA and BTFA adsorbents were well characterized by XRF, FE-SEM with EDX, FTIR, and surface area and porosity measurement which proves the chemical constituents, functional groups and morphology of the adsorbents. The catechol adsorption capacities of synthesized BTFA and native material were determined. The adsorption was slightly increased with an increase in pH value. The monolayer adsorption capacities of FA and BTFA for catechol were 100 mg g⁻¹ and 333.33 mg g⁻¹ respectively, and maximum adsorption occurs within 60 minutes for both adsorbents used in this test. The equilibrium data are fitted by Freundlich isotherm found on the basis of error analysis (RMSE, SSE, and χ²). Adsorption was found to be spontaneous and exothermic on the basis of thermodynamic parameters (ΔG°, ΔS°, and ΔH°). Pseudo-second-order kinetic model better fitted the data for both FA and BTFA. BTFA showed large adsorptive characteristics, high separation selectivity, and excellent recyclability than FA. These findings indicate that BTFA could be employed as an effective and inexpensive adsorbent for the removal of catechol from wastewater.

Keywords: catechol, fly ash, isotherms, kinetics, thermodynamic parameters

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Authors: D. S. Gomes, A. T. Silva

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Analysis of the uncertainty quantification related to nuclear safety margins applied to the nuclear reactor is an important concept to prevent future radioactive accidents. The nuclear fuel performance code may involve the tolerance level determined by traditional deterministic models producing acceptable results at burn cycles under 62 GWd/MTU. The behavior of nuclear fuel can simulate applying a series of material properties under irradiation and physics models to calculate the safety limits. In this study, theoretical predictions of nuclear fuel failure under transient conditions investigate extended radiation cycles at 75 GWd/MTU, considering the behavior of fuel rods in light-water reactors under reactivity accident conditions. The fuel pellet can melt due to the quick increase of reactivity during a transient. Large power excursions in the reactor are the subject of interest bringing to a treatment that is known as the Fuchs-Hansen model. The point kinetic neutron equations show similar characteristics of non-linear differential equations. In this investigation, the multivariate logistic regression is employed to a probabilistic forecast of fuel failure. A comparison of computational simulation and experimental results was acceptable. The experiments carried out use the pre-irradiated fuels rods subjected to a rapid energy pulse which exhibits the same behavior during a nuclear accident. The propagation of uncertainty utilizes the Wilk's formulation. The variables chosen as essential to failure prediction were the fuel burnup, the applied peak power, the pulse width, the oxidation layer thickness, and the cladding type.

Keywords: logistic regression, reactivity-initiated accident, safety margins, uncertainty propagation

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Authors: Danish Laidin, Peter Gostomski, Aaron Marshall, Carlo Carere

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Groundwater contamination of nitrate (NO3-) is becoming more prevalent in regions of intensive and extensive agricultural activities. Household nitrate removal involves using ion exchange membranes and reverse osmosis (RO) systems, whereas industrial nitrate removal may use organic carbon substrates (e.g. methanol) for heterotrophic microbial denitrification. However, these approaches both require high capital investment and operating costs. In this study, denitrification was demonstrated using bio-electrochemical systems (BESs) inoculated from sediments and microbial enrichment cultures. The BES reactors were operated continuously as microbial electrolytic cells (MECs) with a poised potential of -0.7V and -1.1V vs Ag/AgCl. Three parallel MECs were inoculated using hydrogen-driven denitrifying enrichments, stream sediments, and biofilm harvested from a denitrifying biotrickling filter, respectively. These reactors were continuously operated for over a year as various operating conditions were investigated to determine the optimal conditions for electroactive denitrification. The mass loading rate of nitrate was varied between 10 – 70 mg NO3-/d, and the maximum observed nitrate removal rate was 22 mg NO3- /(cm2∙d) with a current of 2.1 mA. For volumetric load experiments, the dilution rate of 1 mM NO3- feed was varied between 0.01 – 0.1 hr-1 to achieve a nitrate loading rate similar to the mass loading rate experiments. Under these conditions, the maximum rate of denitrification observed was 15.8 mg NO3- /(cm2∙d) with a current of 1.7mA. Hydrogen (H2) was supplied intermittently to investigate the hydrogenotrophic potential of the denitrifying biofilm electrodes. H2 supplementation at 0.1 mL/min resulted in an increase of nitrate removal from 0.3 mg NO3- /(cm2∙d) to 3.4 mg NO3- /(cm2∙d) in the hydrogenotrophically subcultured reactor but had no impact on the reactors which exhibited direct electron transfer properties. Results from this study depict the denitrification performance of the immobilized biofilm electrodes, either by direct electron transfer or hydrogen-driven denitrification, and the contribution of the planktonic cells present in the growth medium. Other results will include the microbial community analysis via 16s rDNA amplicon sequencing, varying the effect of poising cathodic potential from 0.7V to 1.3V vs Ag/AgCl, investigating the potential of using in-situ electrochemically produced hydrogen for autotrophic denitrification and adjusting the conductivity of the feed solution to mimic groundwater conditions. These findings highlight the overall performance of sediment inoculated MECs in removing nitrate and will be used for the future development of sustainable solutions for the treatment of nitrate polluted groundwater.

Keywords: bio-electrochemical systems, groundwater, electroactive denitrification, microbial electrolytic cell

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Authors: Choonoh Lee, Seyeon Park, Dongyun Kang, Jaehyeong Choi, Soojee Kim, Younggeun Kim

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Market Kurly is the first South Korean online grocery retailer that guarantees same-day, overnight shipping. More than 1.6 million customers place an average of 4.7 million orders and add 3 to 14 products into a cart per month. The company has sold almost 30,000 kinds of various products in the past 6 months, including food items, cosmetics, kitchenware, toys for kids/pets, and even flowers. The company is operating and expanding multiple dry, cold, and frozen fulfillment centers in order to store and ship these products. Due to the scale and complexity of the fulfillment, pick-pack-ship processes are planned and operated in batches, and thus, the planning that decides the batch of the customers’ orders is a critical factor in overall productivity. This paper introduces a metaheuristic optimization method that reduces the complexity of batch processing in a fulfillment center. The method is an iterative genetic algorithm with heuristic creation and evolution strategies; it aims to group similar orders into pick-pack-ship batches to minimize the total number of distinct products. With a well-designed approach to create initial genes, the method produces streamlined plans, up to 13.5% less complex than the actual plans carried out in the company’s fulfillment centers in the previous months. Furthermore, our digital-twin simulations show that the optimized plans can reduce 3% of operation time for packing, which is the most complex and time-consuming task in the process. The optimization method implements a multithreading design on the Spring framework to support the company’s warehouse management systems in near real-time, finding a solution for 4,000 orders within 5 to 7 seconds on an AWS c5.2xlarge instance.

Keywords: fulfillment planning, genetic algorithm, online grocery retail, optimization

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Authors: Nehal F. Hassib, Rasha M. El Hossini, Inas M. Sayed, Maha R. Abouzeid, Nermeen A. Bayoumi, Aida M. Mosaad, Lamia K. Gadallah, Moataz Bellah A. T. Abdelbari, Heba A. El-Sayed, Hasnaa Elbendary, Ghada Abdel-Salam, Maha Zaki, Mostafa I. Mostafa, Mohamed S. Abdel-Hamid

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Enamel, the outermost layer of the tooth crown, is the hardest dental tissue and serves as a protective barrier. Amelogenesis, the process of enamel formation, is regulated by multiple genes to ensure normal, defect-free enamel. Defective enamel manifests as hypoplasia or as amelogenesis imperfecta (AI), which may occur in isolation or as part of a syndrome. This study presents 29 patients from 18 unrelated families (16 females and 13 males) who exhibited distinctive enamel abnormalities. We conducted thorough clinical examinations and requested laboratory and radiological investigations. Blood samples were collected for molecular analysis, utilizing a targeted panel for known AI variants and whole exome sequencing for unknown variants. Eleven variants linked to enamel anomalies were identified: four genes associated with isolated AI (WDR72, ACP4, SLC24A4, and FAM83H) and seven associated with syndromic forms, including enamel renal syndrome (FAM20A), tricho-dento-osseous syndrome (DLX3), Jalili syndrome (CNNM4), and others linked to neurological and mitochondrial disorders, skeletal dysplasia, and peroxisome disorders. Abnormal oral and dental phenotypes in individuals may indicate serious inherited disorders. Enamel defects have significant implications for aesthetics, function, and patients' psychological well-being. Dental examination, alongside clinical and molecular investigations, is crucial for the accurate diagnosis and prediction of inherited conditions.

Keywords: amelogenesis imperfecta, enamel defect, Enamel renal syndrome, DLX3, Jalili syndrome, WDR72, FAM83H, whole exome sequencing

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Authors: Kushal Gowda Jayaram, Joseph Huret, Jonathan Quibel, Walter-John Chitty, Gilbert Henaff

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Thermal aging is one of the concerns for the long-term operation of nuclear power plants. Indeed, components in the primary circuit undergo thermal aging while exposed to the chemically active environment of Pressurized Water Reactors (PWRs) over time. Among the materials used in the reactor components, Alloy 690 can be found in some critical components for nuclear safety. Despite its importance, research on the effect of thermal aging on the microstructural changes and low cycle fatigue (LCF) behavior of Alloy 690 remains limited. This study aims to assess the impact of thermal aging on the fatigue life of Alloy 690. The as-received sample underwent aging at 420°C for 4000 hours, representing the equivalent aging of 60 years in reactor working conditions. First, the characterization of the area and density of intergranular and intragranular precipitates was performed to understand the microstructural changes in the aged specimen. Then, low cycle fatigue tests were conducted on the as received and aged samples at varying strain amplitudes. To investigate the influence of thermal aging on the fatigue behavior of Alloy 690, fracture surfaces were analyzed to estimate fatigue crack growth rates based on striation spacing measurements. Additionally, the axially cut fractured samples have undergone analysis using Electron Backscatter Diffraction (EBSD) to understand the effect of aging on strain localization near the crack path. Results indicate that while the characterization of the area and density of intergranular precipitates in the aged specimen (for 2000 hours, approximately 30 years) showed no significant changes, there was a slight increase in the area and density of intragranular precipitates under the same conditions.

Keywords: alloy 690, thermal aging, low cycle fatigue, precipitates

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Authors: Narsimhulu Sanke, D. N. Reddy

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The paper is to discuss about the influence of the temperature in the advanced biomass gasifier for gasification, when tested four different biomass fuels individually in the gasification laboratory of Centre for Energy Technology (CET). The gasifier is developed in CET to test any kind of biomass fuel for gasification without changing the gasifier. The gasifier can be used for batch operations and observed and found that there were no operational problems.

Keywords: biomass fuels, temperature, advanced downdraft gasifier, tar, renewable energy sources

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Authors: Yeidy Sorani Montenegro Camacho, Samir Bensaid, Nunzio Russo, Debora Fino

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LiFeO2 nano-powders were prepared via solution combustion synthesis (SCS) method and were used as carbon gasification catalyst in a reduced atmosphere. The gasification of soot with CO2 and H2O in the presence of CO and H2 (syngas atmosphere) were also investigated under atmospheric conditions using a fixed-bed micro-reactor placed in an electric, PID-regulated oven. The catalytic bed was composed of 150 mg of inert silica, 45 mg of carbon (Printex-U) and 5 mg of catalyst. The bed was prepared by ball milling the mixture at 240 rpm for 15 min to get an intimate contact between the catalyst and soot. A Gas Hourly Space Velocity (GHSV) of 38.000 h-1 was used for the tests campaign. The furnace was heated up to the desired temperature, a flow of 120 mL/min was sent into the system and at the same time the concentrations of CO, CO2 and H2 were recorded at the reactor outlet using an EMERSON X-STREAM XEGP analyzer. Catalytic and non-catalytic soot gasification reactions were studied in a temperature range of 120°C – 850°C with a heating rate of 5 °C/min (non-isothermal case) and at 650°C for 40 minutes (isothermal case). Experimental results show that the gasification of soot with H2O and CO2 are inhibited by the H2 and CO, respectively. The soot conversion at 650°C decreases from 70.2% to 31.6% when the CO is present in the feed. Besides, the soot conversion was 73.1% and 48.6% for H2O-soot and H2O-H2-soot gasification reactions, respectively. Also, it was observed that the carbon gasification in mixed atmosphere, i.e., when simultaneous carbon gasification with CO2 and steam take place, with H2 and CO as co-reagents; the gasification reaction is strongly inhibited by CO and H2, as well has been observed in single atmospheres for the isothermal and non-isothermal reactions. Further, it has been observed that when CO2 and H2O react with carbon at the same time, there is a passive cooperation of steam and carbon dioxide in the gasification reaction, this means that the two gases operate on separate active sites without influencing each other. Finally, despite the extreme reduced operating conditions, it has been demonstrated that the 32.9% of the initial carbon was gasified using LiFeO2-catalyst, while in the non-catalytic case only 8% of the soot was gasified at 650°C.

Keywords: soot gasification, nanostructured catalyst, reducing environment, syngas

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Authors: Aurora Gitto, Philipp Proksch

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The presence of various microorganisms (bacteria, fungi) in surface water and groundwater represents an important issue for human health worldwide. The matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) has emerged as a promising and reliable tool for bacteria identification in clinical diagnostic microbiology and environmental strains thanks to an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. The study aims first to conceptualise and set up library information and create a comprehensive database of MALDI-TOF-MS spectra from environmental water samples. The samples were analysed over a year (2021-2022) using membrane filtration methodology (0.45 μm and 0.22 μm) and then isolated on R2A agar for a period of 5 days and Yeast extract agar growing at 22 °C up to 4 days and 37 °C for 48 hours. The undetected organisms by MALDI-TOF-MS were analysed by PCR and then sequenced. The information obtained by the sequencing was further implemented in the MALDI-TOF-MS library. Among the culturable bacteria, the results show how the incubator temperature affects the growth of some genera instead of others, as demonstrated by Pseudomonas sp., which grows at 22 °C, compared to Bacillus sp., which is abundant at 37 °C. The bacteria community shows a variation in composition also between the media used, as demonstrated with R2A agar which has been defined by a higher presence of organisms not detected compared to YEA. Interesting is the variability of the Genus over one year of sampling and how the seasonality impacts the bacteria community; in fact, in some sampling locations, we observed how the composition changed, moving from winter to spring and summer. In conclusion, the bacteria community in groundwater and river bank filtration represents important information that needs to be added to the library to simplify future water quality analysis but mainly to prevent potential risks to human health.

Keywords: water quality, MALDI-TOF-MS, sequencing, library

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Authors: Othman Elmahdy Othman, Agnés Germot, Daniel Petit, Muhammad Khodary, Abderrahman Maftah

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Recently, the control (D-loop) and cytochrome b (Cyt b) regions of mtDNA have received more attention due to their role in the genetic diversity and phylogenetic studies in different livestock which give important knowledge towards the genetic resource conservation. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. By using cytochrome B sequencing, we aimed to clarify the genetic affinities and phylogeny of six Egyptian sheep breeds. Blood samples were collected from 111 animals belonging to six Egyptian sheep breeds; Barki, Rahmani, Ossimi, Saidi, Sohagi and Fallahi. The total DNA was extracted and the specific primers were used for conventional PCR amplification of the cytochrome B region of mtDNA. PCR amplified products were purified and sequenced. The alignment of sequences was done using BioEdit software and DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 39 polymorphic sites leading to the formation of 29 haplotypes. The haplotype diversity in six tested breeds ranged from 0.643 in Rahmani breed to 0.871 in Barki breed. The lowest genetic distance was observed between Rahmani and Saidi (D: 1.436 and Dxy: 0.00127) while the highest distance was observed between Ossimi and Sohagi (D: 6.050 and Dxy: 0.00534). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of 111 analyzed samples were aligned with references sequences of different haplogroups; A, B, C, D and E. The phylogeny result showed the presence of four haplogroups; HapA, HapB, HapC and HapE in the examined samples whereas the haplogroup D was not found. The result showed that 88 out of 111 tested animals cluster with haplogroup B (79.28%), whereas 12 tested animals cluster with haplogroup A (10.81%), 10 animals cluster with haplogroup C (9.01%) and one animal belongs to haplogroup E (0.90%).

Keywords: phylogeny, genetic biodiversity, MtDNA, cytochrome B, Egyptian sheep

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Authors: Abhaydeep Pandey, Shweta Shukla, Saptamita Goswami, Bhaswati Bandyopadhyay, Vishnampettai Ramachandran, Sudhanshu Vrati, Arup Banerjee

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Dengue virus infection is now considered as one of the most important mosquito-borne infection in human. The virus is known to promote vascular permeability, cerebral edema leading to Dengue hemorrhagic fever (DHF) or Dengue shock syndrome (DSS). Dengue infection has known to be endemic in India for over two centuries as a benign and self-limited disease. In the last couple of years, the disease symptoms have changed, manifesting severe secondary complication. So far, Delhi has experienced 12 outbreaks of dengue virus infection since 1997 with the last reported in 2014-15. Without specific antivirals, the case management of high-risk dengue patients entirely relies on supportive care, involving constant monitoring and timely fluid support to prevent hypovolemic shock. Nonetheless, the diverse clinical spectrum of dengue disease, as well as its initial similarity to other viral febrile illnesses, presents a challenge in the early identification of this high-risk group. WHO recommends the use of warning signs to identify high-risk patients, but warning signs generally appear during, or just one day before the development of severe illness, thus, providing only a narrow window for clinical intervention. The ability to predict which patient may develop DHF and DSS may improve the triage and treatment. With the recent discovery of high throughput RNA sequencing allows us to understand the disease progression at the genomic level. Here, we will collate the results of RNA-Sequencing data obtained recently from PBMC of different categories of dengue patients from India and will discuss the possible role of deregulated genes and long non-coding RNAs NEAT1 for development of disease progression.

Keywords: long non-coding RNA (lncRNA), dengue, peripheral blood mononuclear cell (PBMC), nuclear enriched abundant transcript 1 (NEAT1), dengue hemorrhagic fever (DHF), dengue shock syndrome (DSS)

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Authors: A. Čelan, M. Ćosić, D. Rušić, N. Kuzmanić

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Conducting crystallization in an agitated vessel requires a proper selection of mixing parameters that would result in a production of crystals of specific properties. In dual impeller systems, which are characterized by a more complex hydrodynamics due to the possible fluid flow interactions, revealing a clear link between mixing parameters and crystallization kinetics is still an open issue. The aim of this work is to establish this connection by investigating how fluid flow patterns, generated by two impellers mounted on the same shaft, reflect on metastable zone width of borax decahydrate, one of the most important parameters of the crystallization process. Investigation was carried out in a 15-dm³ bench scale batch cooling crystallizer with an aspect ratio (H/T) equal to 1.3. For this reason, two radial straight blade turbines (4-SBT) were used for agitation. Experiments were conducted at different impeller spacings at the state of complete suspension. During the process of an unseeded batch cooling crystallization, solution temperature and supersaturation were continuously monitored what enabled a determination of the metastable zone width. Hydrodynamic conditions in the vessel achieved at different impeller spacings investigated were analyzed in detail. This was done firstly by measuring the mixing time required to attain the desired level of homogeneity. Secondly, fluid flow patterns generated in a described dual impeller system were both photographed and simulated by VisiMix Turbulent software. Also, a comparison of these two visualization methods was performed. Experimentally obtained results showed that metastable zone width is definitely affected by the hydrodynamics in the crystallizer. This means that this crystallization parameter can be controlled not only by adjusting the saturation temperature or cooling rate, as is usually done, but also by choosing a suitable impeller spacing that will result in a formation of crystals of wanted size distribution.

Keywords: dual impeller crystallizer, fluid flow pattern, metastable zone width, mixing time, radial impeller

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Meenu Joshi, Natalie Naidoo, Farzeen Kader

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Identification of body fluids is an essential step in forensic investigation to aid in crime reconstruction. Tissue-specific differentially methylated regions (tDMRs) of the human genome can be targeted to be used as biomarkers to differentiate between body fluids. The present study was undertaken to establish the methylation status of potential tDMRs in blood, semen, saliva, and vaginal fluid by using methylation-specific PCR (MSP) and bisulfite sequencing (BS). The methylation statuses of 3 potential tDMRS in genes ZNF282, PTPRS, and HPCAL1 were analysed in 10 samples of each body fluid. With MSP analysis, the ZNF282, and PTPRS1 tDMR displayed semen-specific hypomethylation while HPCAL1 tDMR showed saliva-specific hypomethylation. With quantitative analysis by BS, the ZNF282 tDMR showed statistically significant difference in overall methylation between semen and all other body fluids as well as at individual CpG sites (p < 0.05). To evaluate the effect of environmental conditions on the stability of methylation profiles of the ZNF282 tDMR, five samples of each body fluid were subjected to five different forensic simulated conditions (dry at room temperature, wet in an exsiccator, outside on the ground, sprayed with alcohol, and sprayed with bleach) for 50 days. Vaginal fluid showed highest DNA recovery under all conditions while semen had least DNA quantity. Under outside on the ground condition, all body fluids except semen showed a decrease in methylation level; however, a significant decrease in methylation level was observed for saliva. A statistical significant difference was observed for saliva and semen (p < 0.05) for outside on the ground condition. No differences in methylation level were observed for the ZNF282 tDMR under all conditions for vaginal fluid samples. Thus, in the present study ZNF282 tDMR has been identified as a novel and stable semen-specific hypomethylation marker.

Keywords: body fluids, bisulphite sequencing, forensics, tDMRs, MSP

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Authors: Nemat Sokhandan Bashir

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Threats from viruses to agricultural crops could be even larger than the losses caused by the other pathogens because, in many cases, the viral infection is latent but crucial from an epidemic point of view. Wild vegetation can be a source of many viruses that eventually find their destiny in crop plants. Although often asymptomatic in wild plants due to adaptation, they can potentially cause serious losses in crops. Therefore, exploring viruses in wild vegetation is very important. Recently, omics have been quite useful for exploring plant viruses from various plant sources, especially wild vegetation. For instance, we have discovered viruses such as Ambrossia asymptomatic virus I (AAV-1) through the application of metagenomics from Oklahoma Prairie Reserve. Accordingly, extracts from randomly-sampled plants are subjected to high speed and ultracentrifugation to separated virus-like particles (VLP), then nucleic acids in the form of DNA or RNA are extracted from such VLPs by treatment with phenol—chloroform and subsequent precipitation by ethanol. The nucleic acid preparations are separately treated with RNAse or DNAse in order to determine the genome component of VLPs. In the case of RNAs, the complementary cDNAs are synthesized before submitting to DNA sequencing. However, for VLPs with DNA contents, the procedure would be relatively straightforward without making cDNA. Because the length of the nucleic acid content of VPLs can be different, various strategies are employed to achieve sequencing. Techniques similar to so-called "chromosome walking" may be used to achieve sequences of long segments. When the nucleotide sequence data were obtained, they were subjected to BLAST analysis to determine the most related previously reported virus sequences. In one case, we determined that the novel virus was AAV-l because the sequence comparison and analysis revealed that the reads were the closest to the Indian citrus ringspot virus (ICRSV). AAV—l had an RNA genome with 7408 nucleotides in length and contained six open reading frames (ORFs). Based on phylogenies inferred from the replicase and coat protein ORFs of the virus, it was placed in the genus Mandarivirus.

Keywords: wild, plant, novel, metagenomics

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Authors: Mateusz Szul, Tomasz Iluk, Aleksander Sobolewski

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Small-scale, distributed energy systems enabling cogeneration of heat and power based on gasification of sewage sludge, are considered as the most efficient and environmentally friendly ways of their treatment. However, economic aspects of such an investment are very demanding; therefore, for such a small scale sewage sludge gasification installation to be profitable, it needs to be efficient and simple at the same time. The article presents results of research on air gasification of sewage sludge in fixed bed GazEla reactor. Two of the most important aspects of the research considered the influence of the composition of sewage sludge blends with other feedstocks on properties of generated syngas and ash sintering problems occurring at the fixed bed. Different means of the fuel pretreatment and blending were proposed as a way of dealing with the above mentioned undesired characteristics. Influence of RDF (Refuse Derived Fuel) and biomasses in the fuel blends were evaluated. Ash properties were assessed based on proximate, ultimate, and ash composition analysis of the feedstock. The blends were specified based on complementary characteristics of such criteria as C content, moisture, volatile matter, Si, Al, Mg, and content of basic metals in the ash were analyzed, Obtained results were assessed with use of experimental gasification tests and laboratory ISO-procedure for analysis of ash characteristic melting temperatures. Optimal gasification process conditions were determined by energetic parameters of the generated syngas, its content of tars and lack of ash sinters within the reactor bed. Optimal results were obtained for co-gasification of herbaceous biomasses with sewage sludge where LHV (Lower Heating Value) of the obtained syngas reached a stable value of 4.0 MJ/Nm3 for air/steam gasification.

Keywords: ash fusibility, gasification, piston engine, sewage sludge

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Authors: D. Kuvshinov, A. Siswanto, J. Lozano-Parada, W. Zimmerman

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Ozone is well known as a powerful fast reaction rate oxidant. The ozone based processes produce no by-product left as a non-reacted ozone returns back to the original oxygen molecule. Therefore an application of ozone is widely accepted as one of the main directions for a sustainable and clean technologies development. There are number of technologies require ozone to be delivered to specific points of a production network or reactors construction. Due to space constrains, high reactivity and short life time of ozone the use of ozone generators even of a bench top scale is practically limited. This requires development of mini/micro scale ozone generator which can be directly incorporated into production units. Our report presents a feasibility study of a new micro scale rector for ozone generation (MROG). Data on MROG calibration and indigo decomposition at different operation conditions are presented. At selected operation conditions with residence time of 0.25 s the process of ozone generation is not limited by reaction rate and the amount of ozone produced is a function of power applied. It was shown that the MROG is capable to produce ozone at voltage level starting from 3.5kV with ozone concentration of 5.28E-6 (mol/L) at 5kV. This is in line with data presented on numerical investigation for a MROG. It was shown that in compare to a conventional ozone generator, MROG has lower power consumption at low voltages and atmospheric pressure. The MROG construction makes it applicable for emerged and dry systems. With a robust compact design MROG can be used as incorporated unit for production lines of high complexity.

Keywords: dielectric barrier discharge (DBD), micro reactor, ozone, plasma

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Authors: A. Kesraoui, M. Seffen

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Applications of adsorption onto activated carbon for water treatment are well known. The process has been demonstrated to be widely effective for removing dissolved organic substances from wastewaters, but this treatment has a major drawback is the high operating cost. The main goal of our research work is to improve the retention capacity of Tunisian biomass for the depollution of industrial wastewater and retention of pollutants considered toxic. The biosorption process is based on the retention of molecules and ions onto a solid surface composed of biological materials. The evaluation of the potential use of these materials is important to propose as an alternative to the adsorption process generally expensive, used to remove organic compounds. Indeed, these materials are very abundant in nature and are low cost. Certainly, the biosorption process is effective to remove the pollutants, but it presents a slow kinetics. The improvement of the biosorption rates is a challenge to make this process competitive with respect to oxidation and adsorption onto lignocellulosic fibers. In this context, the alternating current appears as a new alternative, original and a very interesting phenomenon in the acceleration of chemical reactions. Our main goal is to increase the retention acceleration of dyes (indigo carmine, methylene blue) and phenol by using a new alternative: alternating current. The adsorption experiments have been performed in a batch reactor by adding some of the adsorbents in 150 mL of pollutants solution with the desired concentration and pH. The electrical part of the mounting comprises a current source which delivers an alternating current voltage of 2 to 15 V. It is connected to a voltmeter that allows us to read the voltage. In a 150 mL capacity cell, we plunged two zinc electrodes and the distance between two Zinc electrodes has been 4 cm. Thanks to alternating current, we have succeeded to improve the performance of activated carbon by increasing the speed of the indigo carmine adsorption process and reducing the treatment time. On the other hand, we have studied the influence of the alternating current on the biosorption rate of methylene blue onto Luffa cylindrica fibers and the hybrid material (Luffa cylindrica-ZnO). The results showed that the alternating current accelerated the biosorption rate of methylene blue onto the Luffa cylindrica and the Luffa cylindrica-ZnO hybrid material and increased the adsorbed amount of methylene blue on both adsorbents. In order to improve the removal of phenol, we performed the coupling between the alternating current and the biosorption onto two adsorbents: Luffa cylindrica and the hybrid material (Luffa cylindrica-ZnO). In fact, the alternating current has succeeded to improve the performance of adsorbents by increasing the speed of the adsorption process and the adsorption capacity and reduce the processing time.

Keywords: adsorption, alternating current, dyes, modeling

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Authors: Fei Sun, Meilan Xu, Jianghui Zhu, Maria Stefanie Dwiyanti, Cheolwoo Park, Fanjiang Kong, Baohui Liu, Tetsuya Yamada, Jun Abe

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Reduced or lack of sensitivity to long daylengths is a key character for soybean, a short-day crop, to adapt to higher latitudinal environments. However, the photoperiod-insensitivity often results in a reduction of the duration of vegetative growth and final yield. To overcome this limitation, a photoperiod insensitive line (RIL16) was developed in this study that delayed flowering from the recombinant inbred population derived from a cross between a photoperiod-insensitive cultivar AGS292 and a late-flowering Thai cultivar K3. Expression analyses under SD and LD conditions revealed that the expression levels of FLOWERING LOCUS T (FT) orthologues, FT2a and FT5a, were lowered in RIL16 relative to AGS292, although the expression of E1, a soybean-specific suppressor for FTs, was inhibited in both conditions. A soybean orthologue of TARGET OF EAT1 (TOE1), another suppressor of FT, showed an upregulated expression in RIL16, which appeared to reflect a lower expression of miR172a. Our data suggest that the delayed flowering of RIL16 most likely is controlled by genes involved in an age-dependent pathway in flowering. The QTL analysis based on 1,125 SNPs obtained from Restriction Site Associated DNA Sequencing revealed two major QTLs for flowering dates in Chromosome 16 and two minor QTLs in Chromosome 4, all of which accounted for 55% and 48% of the whole variations observed in natural day length and artificially-induced long day length conditions, respectively. The intervals of the major QTLs harbored FT2a and FT5a, respectively, on the basis of annotated genes in the Williams 82 reference genome. Sequencing analysis further revealed a nonsynonymous mutation in FT2a and an SNP in the 3′ UTR region of FT5a. A further study may elucidate a detailed mechanism underlying the QTL for late flowering. The alleles from K3 at the two QTLs can be used singly or in combination to retain an appropriate duration of vegetative growth to maximize the final yield of photoperiod-insensitive soybeans.

Keywords: FT genes, miR72a, photoperiod-insensitive, soybean flowering

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Authors: Sakeh N. Mohd, Bahari M. N. Abdul, Abdullah S. N. Akmar

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Oil palm production generates high export earnings to many countries especially in Southeast Asian region. Infection by necrotrophic fungus, Ganoderma boninense on oil palm results in basal stem rot which compromises oil palm production leading to significant economic loss. There are no reliable disease treatments nor promising resistant oil palm variety has been cultivated to eradicate the disease up to date. Thus, understanding molecular mechanisms underlying early interactions of oil palm with Ganoderma boninense may be vital to promote preventive or control measure of the disease. In the present study, four months old oil palm seedlings were infected via artificial inoculation of Ganoderma boninense on rubber wood blocks. Roots of six biological replicates of treated and untreated oil palm seedlings were harvested at 0, 3, 7 and 11 days post inoculation. Next-generation sequencing was performed to generate high-throughput RNA-Seq data and identify differentially expressed genes (DEGs) during early oil palm-Ganoderma boninense interaction. Based on de novo transcriptome assembly, a total of 427,122,605 paired-end clean reads were assembled into 30,654 unigenes. DEGs analysis revealed upregulation of 173 transcription factors on Ganoderma boninense-treated oil palm seedlings. Sixty-one transcription factors were categorized as DEGs according to stringent cut-off values of genes with log2 ratio [Number of treated oil palm seedlings/ Number of untreated oil palm seedlings] ≥ |1.0| (corresponding to 2-fold or more upregulation) and P-value ≤ 0.01. Transcription factors in response to biotic stress will be screened out from abiotic stress using reverse transcriptase polymerase chain reaction. Transcription factors unique to biotic stress will be verified using real-time polymerase chain reaction. The findings will help researchers to pinpoint defense response mechanism specific against Ganoderma boninense.

Keywords: Ganoderma boninense, necrotrophic, next-generation sequencing, transcription factors

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Authors: Abhishek Sraw, Amit Sobti, Yamini Pandey, R. K. Wanchoo, Amrit Pal Toor

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Monocrotophos (MCP) is a widely used pesticide in India, which belong to an extremely toxic organophosphorus family, is persistent in nature and its toxicity is widely reported in all environmental segments in the country. Advanced Oxidation Process (AOP) is a promising solution to the problem of water pollution. TiO₂ is being widely used as a photocatalyst because of its many advantages, but it has a large band gap, due to which it is modified using metal and nonmetal dopant to make it active under sunlight and visible light. The use of nanosized powdered catalysts makes the recovery process extremely complicated. Hence the aim is to use low cost, easily available, eco-friendly clay material in form of bead as the support for the immobilization of catalyst, to solve the problem of post-separation of suspended catalyst from treated water. A recirculation type photocatalytic reactor (RTPR), using ultraviolet light emitting source (blue black lamp) was designed which work effectively for both suspended catalysts and catalyst coated clay beads. The bare, TiO₂ and W-TiO₂ coated clay beads were characterized by scanning electron microscopy (SEM), electron dispersive spectroscopy (EDS) and N₂ adsorption–desorption measurements techniques (BET) for their structural, textural and electronic properties. The study involved variation of different parameters like light conditions, recirculation rate, light intensity and initial MCP concentration under UV and sunlight for the degradation of MCP. The degradation and mineralization studies of the insecticide solution were performed using UV-Visible spectrophotometer, and COD vario-photometer and GC-MS analysis respectively. The main focus of the work lies in checking the recyclability of the immobilized TiO₂ over clay beads in the developed RTPR up to 30 continuous cycles without reactivation of catalyst. The results demonstrated the economic feasibility of the utilization of developed RTPR for the efficient purification of pesticide polluted water. The prepared TiO₂ clay beads delivered 75.78% degradation of MCP under UV light with negligible catalyst loss. Application of W-TiO₂ coated clay beads filled RTPR for the degradation of MCP under sunlight, however, shows 32% higher degradation of MCP than the same system based on undoped TiO₂. The COD measurements of TiO₂ coated beads led to 73.75% COD reduction while W-TiO₂ resulted in 87.89% COD reduction. The GC-MS analysis confirms the efficient breakdown of complex MCP molecules into simpler hydrocarbons. This supports the promising application of clay beads as a support for the photocatalyst and proves its eco-friendly nature, excellent recyclability, catalyst holding capacity, and economic viability.

Keywords: immobilized clay beads, monocrotophos, recirculation type photocatalytic reactor, TiO₂

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