Search results for: bacterial gene clusters

Authors: Aidin Foroutan, David S. Wishart, Leluo L. Guan, Carolyn Fitzsimmons

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Maximizing efficiency and growth potential of beef cattle requires not only genetic selection (i.e. residual feed intake (RFI)) but also adequate nutrition throughout all stages of growth and development. Nutrient restriction during gestation has been shown to negatively affect post-natal growth and development as well as fertility of the offspring. This, when combined with RFI may affect progeny traits. This study aims to investigate the impact of selection for divergent genetic potential for RFI and maternal nutrition during early- to mid-gestation, on bull calf traits such as fertility and muscle development using multiple ‘omics’ approaches. Comparisons were made between High-diet vs. Low-diet and between High-RFI vs. Low-RFI animals. An epigenetics experiment on semen samples identified 891 biomarkers associated with growth and development. A gene expression study on Longissimus thoracis muscle, semimembranosus muscle, liver, and testis identified 4 genes associated with muscle development and immunity of which Myocyte enhancer factor 2A [MEF2A; induces myogenesis and control muscle differentiation] was the only differentially expressed gene identified in all four tissues. An initial metabolomics experiment on serum samples using nuclear magnetic resonance (NMR) identified 4 metabolite biomarkers related to energy and protein metabolism. Once all the biomarkers are identified, bioinformatics approaches will be used to create a database covering all the ‘omics’ data collected from this project. This database will be broadened by adding other information obtained from relevant literature reviews. Association analyses with these data sets will be performed to reveal key biological pathways affected by RFI and maternal nutrition. Through these association studies between the genome and metabolome, it is expected that candidate biomarker genes and metabolites for feed efficiency, fertility, and/or muscle development are identified. If these gene/metabolite biomarkers are validated in a larger animal population, they could potentially be used in breeding programs to select superior animals. It is also expected that this work will lead to the development of an online tool that could be used to predict future traits of interest in an animal given its measurable ‘omics’ traits.

Keywords: biomarker, maternal nutrition, omics, residual feed intake

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Authors: Bavneet Kaur Sidhu, Manoj Tiwari

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Global Developmental Delay (GDD) is a common pediatric condition. Etiologies of GDD might, however, differ in developing countries. In the last decade, sporadic families are being reported in various countries. As to the author’s best knowledge, many risk factors and their correlation with the prevalence of GDD have been studied but its statistical correlation has not been done. Thus we propose the present study by targeting the risk factor, prevalence and their statistical correlation with GDD. FMR1 gene was studied to confirm the disease and its penetrance. A complete questionnaire-based performance was designed for the statistical studies having a personal, past and present medical history along with their socio-economic status as well. Methods: We distributed the children’s age in 4 different age groups having 5-year intervals and applied structural equation modeling (SEM) techniques, Spearman’s rank correlation coefficient, Karl Pearson correlation coefficient, and chi-square test.Result: A total of 1100 families were enrolled for this study; among them, 330 were clinically and biologically confirmed (radiological studies) for the disease, 204 were males (61.8%), 126 were females (38.18%). We found that 27.87% were genetic and 72.12 were sporadic, out of 72.12 %, 43.277% cases from urban and 56.72% from the rural locality, the mothers' literacy rate was 32.12% and working women numbers were 41.21%. Conclusions: There is a significant association between mothers' age and GDD prevalence, which is also followed by mothers' literacy rate and mothers' occupation, whereas there was no association between fathers' age and GDD.

Keywords: global developmental delay, FMR1 gene, spearman’ rank correlation coefficient, structural equation modeling

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Authors: Nurlaili Syafar Wulan, Almurdi, Suprianto Kosno

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Introduction: Periodontitis defined as an inflammatory disease of teeth supporting tissue with irritation of specific pathogens as the main aetiology. Periodontitis can be cured by giving medical action accompanied by administration of an antibiotic, but the use of antibiotic has a side effect that can cause bacterial resistance. This side effect can be corrected by probiotic, which has antibiotic-like substance but do not have bacterial resistance effect; it makes probiotic became a promising future periodontitis medication. West Sumatran people has their own typical traditional food product made from fermented buffalo’s milk called dadih, and it contained probiotics. Objectives: The aim of this study was to determine the ability of probiotic Pediococcus pentosaceus isolated from dadih in inhibiting the growth of bacteria Aggregatibacter actinomycetemcomitans. Material and Method: This was a true experimental study with post-test and control group design. This study was conducted on 36 samples of 2 treatment groups, the test group with probiotic Pediococcus pentosacesus isolated from dadih and the negative control group with sterile aquadest. The antibacterial effect was tested using the Kirby-Bauer disk diffusion method and calculated by measuring the zone of inhibition on MHA around paper disk using a sliding caliper with 0.5 mm accuracy. Result: The result of bivariate analysis using Independent t-test was p=0.00 where p < 0.05 means that there is a significant difference between the tested group and negative control group. Conclusion: Probiotic Pediococcus pentosaceus isolated from dadih are able to inhibit the growth of Aggregatibacter actinomycetemcomitans.

Keywords: aggregatibacter actinomycetemcomitans, antibacterial activities, periodontitis, probiotic Pediococcus pentosaceus

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Authors: Jinchen Cao, Tiantian Du

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As waxy crude oil is easy to crystallization and deposition in the pipeline wall, it causes pipeline clogging and leads to the reduction of oil and gas gathering and transmission efficiency. In this paper, a mesoscopic scale dissipative particle dynamics method is employed, and constructed four pipe wall models, including smooth wall (SW), hydroxylated wall (HW), rough wall (RW), and single-layer graphene wall (GW). Snapshots of the simulation output trajectories show that paraffin molecules interact with each other to form a network structure that constrains water molecules as their nucleation sites. Meanwhile, it is observed that the paraffin molecules on the near-wall side are adsorbed horizontally between inter-lattice gaps of the solid wall. In the pressure range of 0 - 50 MPa, the pressure change has less effect on the affinity properties of SS, HS, and GS walls, but for RS walls, the contact angle between paraffin wax and water molecules was found to decrease with the increase in pressure, while the water molecules showed the opposite trend, the phenomenon is due to the change in pressure, leading to the transition of paraffin wax molecules from amorphous to crystalline state. Meanwhile, the minimum crystalline phase pressure (MCPP) was proposed to describe the lowest pressure at which crystallization of paraffin molecules occurs. The maximum number of crystalline clusters formed by paraffin molecules at MCPP in the system showed NSS (0.52 MPa) > NHS (0.55 MPa) > NRS (0.62 MPa) > NGS (0.75 MPa). The MCPP on the graphene surface, with the least number of clusters formed, indicates that the addition of graphene inhibited the crystallization process of paraffin deposition on the wall surface. Finally, the thermal conductivity was calculated, and the results show that on the near-wall side, the thermal conductivity changes drastically due to the occurrence of adsorption crystallization of paraffin waxes; on the fluid side the thermal conductivity gradually tends to stabilize, and the average thermal conductivity shows: ĸRS(0.254W/(m·K)) > ĸRS(0.249W/(m·K)) > ĸRS(0.218W/(m·K)) > ĸRS(0.188W/(m·K)).This study provides a theoretical basis for improving the transport efficiency and heat transfer characteristics of waxy crude oil in terms of wall type, wall roughness, and MCPP.

Keywords: waxy crude oil, thermal conductivity, crystallization, dissipative particle dynamics, MCPP

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Authors: Claudia Patricia Beltran Miranda, Mónica López Anaya, Mónica Navarro Meza, Maria Leonor Valderrama Chairez

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Background: Mexico occupies the second world-wide place of morbid obese people (10- 12 million). Factors that predispose the development of MO are genetic, environmental, physiological, psycho-social and behavioral (nourishing habits). Objective: Associate Gln223Arg polymorphism of gene LEPR, levels of leptina and nourishing habits with the presence of morbid obesity in adolescents of the south of Jalisco (México). Methods: In 41 adolescents (18 normal weight and 23 morbid obesity) of 12 to 19 years of age, both sexes that were measure size and weight with tanita scale and stadimeter to determine IMC. Morbid obesity was determined by tables of the WHO and was established with a standard deviation >3. The Gln223Arg polymorphism have been identify by PCR and leptina levels by ELISA. Nourishing habits were evaluate by the questionnaire the Adolescent Food Habits Checklist. The statistical analysis was performed to compare mean scores obtained from the questionnaire when we compare morbid obesity vs. normal weight adolescents with p=0.03 and a significance of 95%. Results: frequencies alellics and genics were not stadistics significatives p= 0,011 and p=0,279 respectly when were compared between normal weight adolescents and morbib obesity Leptin levels and nourishing habits were associated with morbid obesity. The polymorphism not shown significance with morbid obesity. Conclusions: Dietary habits and leptin levels in adolescents are important factor that predisposes the development of obesity in adolescents. The presence of the polymorphism are not associated with morbid obesity in these subjects.

Keywords: leptin, nourishing habits, morbid obesity, polymorphism

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Authors: Omaima A. Sharaf, Tarek A. Moussa, Said M. Badr El-Din, H. Moawad

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Background: Polycyclic aromatic hydrocarbons (PAHs) pose great environmental and human health concerns for their widespread occurrence, persistence, and carcinogenic properties. PAHs releases due to anthropogenic activities to the wider environment have led to higher concentrations of these contaminants than would be expected from natural processes alone. This may result in a wide range of environmental problems that can accumulate in agricultural ecosystems, which threatened to become a negative impact on sustainable agricultural development. Thus, this study aimed to evaluate the physico-chemical, and microbial properties of the compost leachate (CL) to assess its role as nutrient and microbial source (biostimulation/bioaugmentation) for developing a cost-effective bioremediation technology for PAHs contaminated sites. Material and Methods: PAHs-degrading bacteria were isolated from CL that was collected from a composting site located in central Scotland, UK. Isolation was carried out by enrichment using phenanthrene (PHR), pyrene (PYR) and benzo(a)pyrene (BaP) as the sole source of carbon and energy. The isolates were characterized using a variety of phenotypic and molecular properties. Six different isolates were identified based on the difference in morphological and biochemical tests. The efficiency of these isolates in PAHs utilization was assessed. Further analysis was performed to define taxonomical status and phylogenic relation between the most potent PAHs-utilizing bacterial strains and other standard strains, using molecular approach by partial 16S rDNA gene sequence analysis. Results indicated that the 16S rDNA sequence analysis confirmed the results of biochemical identification, as both of biochemical and molecular identification of the isolates assigned them to Bacillus licheniformis, Pseudomonas aeruginosa, Alcaligenes faecalis, Serratia marcescens, Enterobacter cloacae and Providenicia which were identified as the prominent PAHs-utilizers isolated from CL. Conclusion: This study indicates that the CL samples contain a diverse population of PAHs-degrading bacteria and the use of CL may have a potential for bioremediation of PAHs contaminated sites.

Keywords: polycyclic aromatic hydrocarbons, physico-chemical analyses, compost leachate, microbial and biochemical analyses, phylogenic relations, 16S rDNA sequence analysis

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Authors: Justine Garraud, Hervé Capiaux, Cécile Le Guern, Pierre Gaudin, Clémentine Lapie, Samuel Chaffron, Erwan Delage, Thierry Lebeau

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The repeated use of Bordeaux mixture (copper sulphate) and other chemical forms of copper (Cu) has led to its accumulation in wine-growing soils for more than a century, to the point of modifying the ecosystem of these soils. Phytoextraction of copper could progressively reduce the Cu load in these soils, and even to recycle copper (e.g. as a micronutrient in animal nutrition) by cultivating the extracting plants in the inter-row of the vineyards. Soil cleaning up usually requires several years because the chemical speciation of Cu in solution is mainly based on forms complexed with dissolved organic matter (DOM) that are not phytoavailable, unlike the "free" forms (Cu2+). Indeed, more than 98% of Cu in the solution is bound to DOM. The selection and inoculation of invineyardsoils in vineyard soils ofbacteria(bioaugmentation) able to degrade Cu-DOM complexes could increase the phytoavailable pool of Cu2+ in the soil solution (in addition to bacteria which first mobilize Cu in solution from the soil bearing phases) in order to increase phytoextraction performance. In this study, sevenCu-accumulating plants potentially usable in inter-row were tested for their Cu phytoextraction capacity in hydroponics (ray-grass, brown mustard, buckwheat, hemp, sunflower, oats, and chicory). Also, a bacterial consortium was tested: Pseudomonas sp. previously studied for its ability to mobilize Cu through the pyoverdine siderophore (complexing agent) and potentially to degrade Cu-DOM complexes, and a second bacterium (to be selected) able to promote the survival of Pseudomonas sp. following its inoculation in soil. Interaction network method was used based on the notions of co-occurrence and, therefore, of bacterial abundance found in the same soils. Bacteria from the EcoVitiSol project (Alsace, France) were targeted. The final step consisted of incoupling the bacterial consortium with the chosen plant in soil pots. The degradation of Cu-DOMcomplexes is measured on the basis of the absorption index at 254nm, which gives insight on the aromaticity of the DOM. The“free” Cu in solution (from the mobilization of Cu and/or the degradation of Cu-MOD complexes) is assessed by measuring pCu. Eventually, Cu accumulation in plants is measured by ICP-AES. The selection of the plant is currently being finalized. The interaction network method targeted the best positive interactions ofFlavobacterium sp. with Pseudomonassp. These bacteria are both PGPR (plant growth promoting rhizobacteria) with the ability to improve the plant growth and to mobilize Cu from the soil bearing phases (siderophores). Also, these bacteria are known to degrade phenolic groups, which are highly present in DOM. They could therefore contribute to the degradation of DOM-Cu. The results of the upcoming bacteria-plant coupling tests in pots will be also presented.

Keywords: complexes Cu-DOM, bioaugmentation, phytoavailability, phytoextraction

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Authors: Agne Jucyte Cicine, Vytautas Abromaitis, Zita Rasuole Gasiunaite, I. Vybernaite-Lubiene, D. Overlinge, K. Vilke

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Pharmaceutical pollution in aquatic environments has become a growing concern. Various active pharmaceutical ingredient (API) residues, hormones, antibiotics, or/and psychiatric drugs, have already been discovered in different environmental compartments. Due to existing ineffective wastewater treatment technologies to remove APIs, an underestimated amount can enter the ecosystem by discharged treated wastewater. Especially, psychiatric compounds, such as carbamazepine (CBZ) and venlafaxine (VNX), persist in effluent even post-treatment. Therefore, these pharmaceuticals usually exceed safe environmental levels and pose risks to the aquatic environment, particularly to sensitive ecosystems such as the Baltic Sea. CBZ, known for its chemical stability and long biodegradation time, accumulates in the environment, threatening aquatic life and human health through the food chain. As the use of medication rises, there is an urgent need for advanced wastewater treatment to reduce pharmaceutical contamination and meet future regulatory requirements. In this study, we tested advanced oxidation technology using ozone to remove two commonly used psychiatric drugs (carbamazepine and venlafaxine) from biologically treated wastewater effluent. Additionally, general water quality parameters (suspended matter (SPM), dissolved organic carbon (DOC), chemical oxygen demand (COD), and bacterial presence were analyzed. Three wastewater treatment plants (WWTPs) representing different anthropogenic pressures were selected: 1) resort, 2) resort and residential, and 3) residential, industrial, and resort. Wastewater samples for the experiment were collected during the summer season after mechanical and biological treatment and ozonated for 5, 10, and 15 minutes. The initial dissolved ozone concentration of 7,3±0,7 mg/L was held constant during all the experiments. Pharmaceutical levels in this study exceeded the predicted no-effect concentration (PNEC) of 500 and 90 ng L⁻¹ for CBZ and VNX, respectively, in all WWTPs, except CBZ in WWTP 1. Initial CBZ contamination was found to be lower in WWTP 1 (427.4 ng L⁻¹), compared with WWTP 2 (1266.5 ng L⁻¹) and 3 (119.2 ng L⁻¹). VNX followed a similar trend with concentrations of 341.2 ng L⁻¹, 361.4 ng L⁻¹, and 390.0 ng L⁻¹, respectively, for WWTPs 1, 2, and 3. It was determined that CBZ was not detected in the effluent after 5 minutes of ozonation in any of the WWTPs. Contrarily, VNX was still detected after 5, 10, and 15 minutes of treatment with ozone, however, under the limits of quantification (LOD) (<5ng L⁻¹). Additionally, general pollution of SPM, DOC, COD, and bacterial contamination was reduced notably after 5 minutes of treatment with ozone, while no bacterial growth was obtained. Although initial pharmaceutical levels exceeded PNECs, indicating ongoing environmental risks, ozonation demonstrated high efficiency in reducing pharmaceutical and general contamination in wastewater with different pollution matrices.

Keywords: Baltic Sea, ozonation, pharmaceuticals, wastewater treatment plants

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Authors: M. S. Matlala, I. Ignatious

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Environmental sustainability has taken the center stage in human life all over the world. Energy is the most essential component of our life. The conventional sources of energy are non-renewable and have a detrimental environmental impact. Therefore, there is a need to move from conventional to non-conventional renewable energy sources to satisfy the world’s energy demands. The study aimed at screening for microbial cellulolytic enzymes using a proteomic approach. The objectives were to screen for microbial cellulases with high specific activity and separate the cellulolytic enzymes using a combination of zymography and two-dimensional (2-D) gel electrophoresis followed by tryptic digestion, Matrix-assisted Laser Desorption Ionisation-Time of Flight (MALDI-TOF) and bioinformatics analysis. Fungal and bacterial isolates were cultured in M9 minimal and Mandel media for a period of 168 hours at 60°C and 30°C with cellobiose and Avicel as carbon sources. Microbial cells were separated from supernatants through centrifugation, and the crude enzyme from the cultures was used for the determination of cellulase activity, zymography, SDS-PAGE, and two-dimensional gel electrophoresis. Five isolates, with lytic action on carbon sources studied, were a bacterial strain (BARK) and fungal strains (VCFF1, VCFF14, VCFF17, and VCFF18). Peak cellulase production by the selected isolates was found to be 3.8U/ml, 2.09U/ml, 3.38U/ml, 3.18U/ml, and 1.95U/ml, respectively. Two-dimensional gel protein maps resulted in the separation and quantitative expression of different proteins by the microbial isolates. MALDI-TOF analysis and database search showed that the expressed proteins in this study closely relate to different glycoside hydrolases produced by other microbial species with an acceptable confidence level of 100%.

Keywords: cellulases, energy, two-dimensional gel electrophoresis, matrix-assisted laser desorption ionisation-time of flight, MALDI-TOF MS

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Authors: Sirikwan Ponprateep, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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A Kazal-type serine proteinase inhibitor, SPIPm2, was abundantly expressed in the hemocytes and secreted into shrimp plasma has anti-viral property against white spot syndrome virus (WSSV). To discover the molecular mechanism of antiviral activity, the binding assay showed that SPIPm2 bind to the components of viral particle and shrimp hemocyte. From our previous report, viral target protein of SPIPm2 was identified, namely WSV477 using yeast two-hybrid screening. WSV477 is an early gene product of WSSV and involved in viral propagation. In this study, the co-immunoprecipitation technique and Tandem Mass Spectrometry (LC-MS/MS) was used to identify the target protein of SPIPm2 from shrimp hemocyte. The target protein of SPIPm2 was cyclophilin A. In vertebrate, cyclophilin A or peptidylprolyl isomerase A was reported to be the immune suppressor interacted with cyclosporin A involved in immune defense response. The recombinant cyclophilin A from Penaeus monodon (rPmCypA) was produced in E.coli system and purified using Ni-NTA column to confirm the protein-protein interaction. In vitro pull-down assay showed the interaction between rSPIPm2 and rPmCypA. To study the biological function of these proteins, the expression analysis of immune gene in shrimp defense pathways will be investigated after rPmCypA administration.

Keywords: cyclophilin A, protein-protein interaction, Kazal-type serine proteinase inhibitor, Penaeus monodon

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Authors: Zhaoxu Lu, Yufeng Ma, Linying Gao, Li Wang, Mei Qiang

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Mercury (Hg) is a well-recognized environmental pollutant known by its toxicity of development and neurotoxicity, which may result in adverse health outcomes. However, the mechanisms underlying the teratogenic effects of Hg are not well understood. Imprinting genes are emerging regulators for fetal development subject to environmental pollutants impacts. In this study, we examined the association between paternal preconception Hg exposures and the alteration of DNA methylation of imprinting genes in human sperm DNA. A total of 618 men aged from 22 to 59 was recruited from the Reproductive Medicine Clinic of Maternal and Child Care Service Center and the Urologic Surgery Clinic of Shanxi Academy of Medical Sciences during April 2015 and March 2016. Demographic information was collected using questionnaires. Urinary Hg concentrations were measured using a fully-automatic double-channel hydride generation atomic fluorescence spectrometer. And methylation status in the DMRs of imprinting genes H19, Meg3 and Peg3 of sperm DNA were examined by bisulfite pyrosequencing in 243 participants. Spearman’s rank and multivariate regression analysis were used for correlation analysis between sperm DNA methylation status of imprinting genes and urinary Hg levels. The median concentration of Hg for participants overall was 9.09μg/l (IQR: 5.54 - 12.52μg/l; range = 0 - 71.35μg/l); no significant difference was found in median concentrations of Hg among various demographic groups (p > 0.05). The proportion of samples that a beyond intoxication criterion (10μg/l) for urinary Hg was 42.6%. Spearman’s rank correlation analysis indicates a negative correlation between urinary Hg concentrations and average DNA methylation levels in the DMRs of imprinted genes H19 (rs=﹣0.330, p = 0.000). However, there was no such a correlation found in genes of Peg3 and Meg3. Further, we analyzed of correlation between methylation level at each CpG site of H19 and Hg level, the results showed that three out of 7 CpG sites on H19 DMR, namely CpG2 (rs =﹣0.138, p = 0.031), CpG4 (rs =﹣0.369, p = 0.000) and CpG6 (rs=﹣0.228, p = 0.000), demonstrated a significant negative correlation between methylation levels and the levels of urinary Hg. After adjusting age, smoking, drinking, intake of aquatic products and education by multivariate regression analysis, the results have shown a similar correlation. In summary, mercury nonoccupational environmental exposure in reproductive-aged men associated with altered DNA methylation outcomes at DMR of imprinting gene H19 in sperm, implicating the susceptibility of the developing sperm for environmental insults.

Keywords: epigenetics, genomic imprinting gene, DNA methylation, mercury, transgenerational effects, sperm

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Authors: Maria L. G. Lourenco, Viviane Y. Hibaru, Keylla H. N. P. Pereira, Fabiana F. Souza, Joao C. P. Ferreira, Simone B. Chiacchio, Luiz H. A. Machado

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Neonatal conjunctivitis, or ophthalmia, is an infection of the conjunctiva or cornea before opening the eyelids. It is believed that immunodeficiency contributes to the development of the condition. This study aims at reporting a case of ophthalmia neonatorum in a dog, in addition to its diagnosis and treatment. A litter of five pug neonates was admitted to the Sao Paulo State University (UNESP) Veterinary Hospital, Botucatu, Sao Paulo, Brazil, with complaints of ocular secretion. The neonates were five days old. The clinical examination revealed that three newborns presented swelling in the ocular region and a purulent secretion in the medial corner of the eye that was exerting pressure on the ocular globes, which are compatible with the description of this disease. The diagnosis was made based on the clinical signs and bacterial culture of the secretion, which revealed the presence of bacteria belonging to the genus Staphylococcus sp. The laboratory assays did not reveal any alterations. The treatment was instituted gently, opening the eyelids early and cleaning the purulent ocular secretion with saline solution. An ophthalmic ointment with retinol, amino acids, methionine, and chloramphenicol (Epitezan®) was prescribed four times a day for seven days. Blood plasma (2 mL/100 g) was administered subcutaneously because bacterial infections in neonates may represent a failure in the transference of passive immunity. A more thorough cleaning of the environment was also recommended. Neonatal conjunctivitis has a simple diagnosis and treatment. If not treated early, it can evolve to adherence of the eyelids to the cornea, ulceration, and perforation of the cornea. Therefore, the prognosis is favorable as long as the condition is diagnosed early, and the treatment is instituted quickly.

Keywords: ophthalmia neonatorum, neonatal infection, puppy, newborn

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Authors: Sina Gharevali

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Staphylococcus aureus is one of the most important factors for nosocomial infections and infections acquired in a hospital setting role as is. Drug-resistant bacteria methicillin, which in 1961 was reported in many parts of the world, Made the role as the last drug, vancomycin, in the treatment of infections caused by the Staphylococcus aureus chain be taken into consideration. The aim of this study was to evaluate the antimicrobial effects of copper nanoparticles and compared it with antibiotics on Staphylococcus aureus resistant to vancomycin in vitro and animal model. In this study, this test was performed, and the most effective antibiotic for vancomycin-resistant Staphylococcus aureus was determined by disk diffusion method. After various concentrations of copper nanoparticles and antibiotics were prepared and vancomycin resistant Staphylococcus aureus bacteria with serial dilution method for determining antibiotic ciprofloxacin. Minimum Inhibitory Concentration and Minimum Bactericidal Concentrationcopper nanoparticles was performed. The agar dilution method for bacterial growth in different concentrations of copper nanoparticles and antibiotics ciprofloxacin was performed. The agar dilution method for bacterial growth in different concentrations of copper nanoparticles and antibiotics ciprofloxacin was performed. Then the broth dilution method for the antibiotic ciprofloxacin, nano-particles, and nano-particles of copper and copper-established antibiotic synergy MIC and MBC were obtained. MBC was obtained from the experimental animal model test method, and the results were compared. The results showed that copper nanoparticles compared with the antibiotic ciprofloxacin in vitro and animal model more effective in inhibiting the growth of Staphylococcus aureus resistant to vancomycin and ciprofloxacin and extent of the impact of the Synthetic effect of lower copper nanoparticles. Which can then be used to treat clinical research as a candidate.

Keywords: nanoparticles, copper, staphylococcus, aureus

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Authors: Tiziana Ferrero-Regis, Marissa Lindquist

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Circular Economy (CE) is increasingly seen as the reorganisation of production and consumption, and cities are acknowledged as the sources of many ecological and social problems; at the same time, they can be re-imagined through an ecologically and socially resilient future. The concept of the CE has received pointed critiques for its techno-deterministic orientation, focus on science and transformation by the policy. At the heart of our local re-imagining of the CE into circularity through contact zones there is the acknowledgment of collective, spontaneous and shared imaginations of alternative and sustainable futures through the creation of networks of community initiatives that are transformative, creating opportunities that simultaneously make cities rich and enrich humans. This paper presents a mapping project of the fashion and textile ecosystem in Brisbane, Queensland, Australia. Brisbane is currently the most aspirational city in Australia, as its population growth rate is the highest in the country. Yet, Brisbane is considered the least “fashion city” in the country. In contrast, the project revealed a greatly enhanced picture of distinct fashion and textile clusters across greater Brisbane and the adjacency of key services that may act to consolidate CE community contact zones. Clusters to the north of Brisbane and several locales to the south are zones of a greater mix between public/social amenities, walkable zones and local transport networks with educational precincts, community hubs, concentration of small enterprises, designers, artisans and waste recovery centers that will help to establish knowledge of key infrastructure networks that will support enmeshing these zones together. The paper presents two case studies of independent designers who work on new and re-designed clothing through recovering pre-consumer textiles and that operate from within creative precincts. The first case is designer Nelson Molloy, who recently returned to the inner city suburb of West End with their Chasing Zero Design project. The area was known in the 1980s and 1990s for its alternative lifestyle with creative independent production, thrifty clothing shops, alternative fashion and a socialist agenda. After 30 years of progressive gentrification of the suburb, which has dislocated many of the artists, designers and artisans, West End is seeing the return and amplification of clusters of artisans, artists, designers and architects. The other case study is Practice Studio, located in a new zone of creative growth, Bowen Hills, north of the CBD. Practice Studio combines retail with a workroom, offers repair and remaking services, becoming a point of reference for young and emerging Australian designers and artists. The paper demonstrates the spatial politics of the CE and the way in which new cultural capital is produced thanks to cultural specificities and resources. It argues for the recognition of contact zones that are created by local actors, communities and knowledge networks, whose grass-roots agency is fundamental for the co-production of CE’s systems of local governance.

Keywords: contact zones, circular citities, fashion and textiles, circular neighbourhoods, australia

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Authors: Oloruntegbe Kunle Oke, Alake Ese Monica, Odutuyi Olubu Musili

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This research explores the differing effectiveness of cascade and cluster models in professional development programs for educators in Ondo State, Nigeria. The cascade model emphasizes a top-down approach, where training is cascaded from expert trainers to lower levels of teachers. In contrast, the cluster model, a bottom-up approach, fosters collaborative learning among teachers within specific clusters. Through a review of the literature and empirical studies of the implementations of the former in two academic sessions followed by the cluster model in another two, the study examined their effectiveness on teacher development, productivity and students’ achievements. The study also drew a comparative analysis of the strengths and weaknesses associated with each model, considering factors such as scalability, cost-effectiveness, adaptability in various contexts, and sustainability. 2500 teachers from Ondo State Primary Schools participated in the cascade with intensive training in five zones for a week each in two academic sessions. On the other hand, 1,980 and 1,663 teachers in 52 and 34 clusters, respectively, were in the first and the following session. The programs were designed for one week of rigorous training of teachers by facilitators in the former while the latter was made up of four components: sit-in-observation, need-based assessment workshop, pre-cluster and the actual cluster meetings in addition to sensitization, and took place one day a week for ten weeks. Validated Cluster Impact Survey Instruments, CISI and Teacher’s Assessment Questionnaire (TAQ) were administered to ascertain the effectiveness of the models during and after implementation. The findings from the literature detailed specific effectiveness, strengths and limitations of each approach, especially the potential for inconsistencies and resistance to change. Findings from the data collected revealed the superiority of the cluster model. Response to TAQ equally showed content knowledge and skill update in both but were more sustained in the cluster model. Overall, the study contributes to the ongoing discourse on effective strategies for improving teacher training and enhancing student outcomes, offering practical recommendations for the development and implementation of future professional development projects.

Keywords: cascade model, cluster model, teachers’ development, productivity, students’ achievement

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Authors: Ziyue Zeng

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Bacteriophages are viruses which infect bacteria specifically. Over the past decades, phage λ has been extensively studied, especially its interaction with the Escherichia coli LamB (EcLamB) protein receptor. Nonetheless, despite the enormous numbers and near-ubiquity of environmental phages, aside from phage λ, there is a paucity of information on other phages which target EcLamB as a receptor. In this study, to answer the question of whether there are other EcLamB-targeting phages in the natural environment, a simple and convenient method was developed and used for isolating environmental phages which target a particular surface structure of a particular bacterium; in this case, the EcLamB outer membrane protein. From the enrichments with the engineered bacterial hosts, a collection of EcLamB-targeting phages (ΦZZ phages) were easily isolated. Intriguingly, unlike phage λ, an obligate EcLamB-dependent phage in the Siphoviridae family, the newly isolated ΦZZ phages alternatively recognised EcLamB or E. coli OmpC (EcOmpC) as a receptor when infecting E. coli. Furthermore, ΦZZ phages were suggested to represent new species in the Tequatrovirus genus in the Myoviridae family, based on phage morphology and genomic sequences. Most phages are thought to have a narrow host range due to their exquisite specificity in receptor recognition. With the ability to optionally recognise two receptors, ΦZZ phages were considered relatively promiscuous. Via the heterologous expression of EcLamB on the bacterial cell surface, the host range of ΦZZ phages was further extended to three different enterobacterial genera. Besides, an interesting selection of evolved phage mutants with a broader host range was isolated, and the key mutations involved in their evolution to adapt to new hosts were investigated by genomic analysis. Finally, and importantly, two ΦZZ phages were found to be putative generalised transducers, which could be exploited as tools for DNA manipulations.

Keywords: environmental microbiology, phage, microbe-host interactions, microbial ecology

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Authors: Wissam Saliba, Mandy Nicholson

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Secretory carcinoma (SC) is a rare type of salivary gland cancer. It was first realized as a distinct type of malignancy in 2010and wasinitially termed “mammary analogue secretory carcinoma” because of similarities with secretory breast cancer. The name was later changed to SC. Most SCs originate in parotid glands, and most harbour a rare gene mutation: ETV6-NTRK3. This mutation is rare in common cancers and common in rare cancers; it is present in most secretory carcinomas. Disease outcomes for SC are usually described as favourable as many cases of SC are lowgrade (LG), and cancer growth is slow. In early stages, localized therapy is usually indicated (surgery and/or radiation). Despitea favourable prognosis, a sub-set of casescan be much more aggressive.These cases tend to be of high-grade(HG).HG casesare associated with a poorer prognosis.Management of such cases can be challenging due to limited evidence for effective systemic therapy options. This case report describes the clinical management of a 46-year-oldmale patient with a unique case of SC. He was initially diagnosed with a low/intermediate grade carcinoma of the left parotid gland in 2009; he was treated with surgery and adjuvant radiation. Surgical pathology favoured primary salivary adenocarcinoma, and 2 lymph nodes were positive for malignancy. SC was not yet realized as a distinct type of cancerat the time of diagnosis, and the pathology reportvalidated this gap by stating that the specimen lacked features of the defined types of salivary carcinoma.Slow-growing pulmonary nodules were identified in 2017. In 2020, approximately 11 years after the initial diagnosis, the patient presented with malignant pleural effusion. Pathology from a pleural biopsy was consistent with metastatic poorly differentiated cancer of likely parotid origin, likely mammary analogue secretory carcinoma. The specimen was sent for Next Generation Sequencing (NGS); ETV6-NTRK3 gene fusion was confirmed, and systemic therapy was initiated.One cycle ofcarboplatin/paclitaxel was given in June 2020. He was switched to Larotrectinib (NTRK inhibitor (NTRKi)) later that month. Larotrectinib continued for approximately 9 months, with discontinuation in March 2021 due to disease progression. A second-generation NTRKi (Selitrectinib) was accessed and prescribedthrough a single patient study. Selitrectinib was well tolerated. The patient experienced a complete radiological response within~4 months. Disease progression occurred once again in October 2021. Progression was slow, and Selitrectinib continuedwhile the medical team performed a thorough search for additional treatment options. In January 2022, a liver lesion biopsy was performed, and NGS showed an NTRKG623R solvent-front resistance mutation. Various treatment pathways were considered. The patient pursuedanother investigational NTRKi through a clinical trial, and Selitrectinib was discontinued in July 2022. Excellent performance status was maintained throughout the entire course of treatment.It can be concluded that NTRK inhibitors provided satisfactory treatment efficacy and tolerance for this patient with high-grade transformation and NTRK gene fusion cancer. In the future, more clinical research is needed on systemic treatment options for high-grade transformations in NTRK gene fusion SCs.

Keywords: secretory carcinoma, high-grade transformations, NTRK gene fusion, NTRK inhibitor

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Authors: Hamza Javar Magnier, Leslie V. Woodcock

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We report extensive molecular dynamics (MD) computational investigations into the thermodynamic description of supercritical properties for a model fluid that is the simplest realistic representation of atoms or molecules. The pair potential is a hard-sphere repulsion of diameter σ with a very short attraction of length λσ. When λ = 1.005 the range is so short that the model atoms are referred to as “adhesive spheres”. Molecular dimers, trimers …etc. up to large clusters, or droplets, of many adhesive-sphere atoms are unambiguously defined. This then defines percolation transitions at the molecular level that bound the existence of gas and liquid phases at supercritical temperatures, and which define the existence of a supercritical mesophase. Both liquid and gas phases are seen to terminate at the loci of percolation transitions, and below a second characteristic temperature (Tc2) are separated by the supercritical mesophase. An analysis of the distribution of clusters in gas, meso- and liquid phases confirms the colloidal nature of this mesophase. The general phase behaviour is compared with both experimental properties of the water-steam supercritical region and also with formally exact cluster theory of Mayer and Mayer. Both are found to be consistent with the present findings that in this system the supercritical mesophase narrows in density with increasing T > Tc and terminates at a higher Tc2 at a confluence of the primary percolation loci. The expended plot of the MD data points in the mesophase of 7 critical and supercritical isotherms in highlight this narrowing in density of the linear-slope region of the mesophase as temperature is increased above the critical. This linearity in the mesophase implies the existence of a linear combination rule between gas and liquid which is an extension of the Lever rule in the subcritical region, and can be used to obtain critical parameters without resorting to experimental data in the two-phase region. Using this combination rule, the calculated critical parameters Tc = 0.2007 and Pc = 0.0278 are found be agree with the values found by of Largo and coworkers. The properties of this supercritical mesophase are shown to be consistent with an alternative description of the phenomenon of critical opalescence seen in the supercritical region of both molecular and colloidal-protein supercritical fluids.

Keywords: critical opalescence, supercritical, square-well, percolation transition, critical parameters.

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Authors: Franco Van De Velde, Debora Esposito, Maria E. Pirovani, Mary A. Lila

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The physiology of various inflammatory diseases is a complex process mediated by inflammatory and immune cells such as macrophages and monocytes. Chronic inflammation, as observed in many cardiovascular and autoimmune disorders, occurs when the low-grade inflammatory response fails to resolve with time. Because of the complexity of the chronic inflammatory disease, major efforts have focused on identifying novel anti-inflammatory agents and dietary regimes that prevent the pro-inflammatory process at the early stage of gene expression of key pro-inflammatory mediators and cytokines. The ability of the extracts of three blackberry cultivars (‘Jumbo’, ‘Black Satin’ and ‘Dirksen’), and one strawberry cultivar (‘Camarosa’) to inhibit four well-known genetic biomarkers of inflammation: inducible nitric oxide synthase (iNOS), cyclooxynase-2 (Cox-2), interleukin-1β (IL-1β) and interleukin-6 (IL-6) in an in vitro lipopolysaccharide-stimulated murine RAW 264.7 macrophage model were investigated. Moreover, the effect of latter extracts on the intracellular reactive oxygen species (ROS) and nitric oxide (NO) production was assessed. Assay was conducted with 50 µg/mL crude extract concentration, an amount that is easily achievable in the gastrointestinal tract after berries consumption. The mRNA expression levels of Cox-2 and IL-6 were reduced consistently (more than 30%) by extracts of ‘Jumbo’ and ‘Black Satin’ blackberries. Strawberry extracts showed high reduction in mRNA expression levels of IL-6 (more than 65%) and exhibited moderate reduction in mRNA expression of Cox-2 (more than 35%). The latter behavior mirrors the intracellular ROS production of the LPS stimulated RAW 264.7 macrophages after the treatment with blackberry ‘Black Satin’ and ‘Jumbo’, and strawberry ‘Camarosa’ extracts, suggesting that phytochemicals from these fruits may play a role in the health maintenance by reducing oxidative stress. On the other hand, effective inhibition in the gene expression of IL-1β and iNOS was not observed by any of blackberry and strawberry extracts. However, suppression in the NO production in the activated macrophages among 5–25% was observed by ‘Jumbo’ and ‘Black Satin’ blackberry extracts and ‘Camarosa’ strawberry extracts, suggesting a higher NO suppression property by phytochemicals of these fruits. All these results suggest the potential beneficial effects of studied berries as functional foods with antioxidant and anti-inflammatory roles. Moreover, the underlying role of phytochemicals from these fruits in the protection of inflammatory process will deserve to be further explored.

Keywords: cyclooxygenase-2, functional foods, interleukin-6, reactive oxygen species

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Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

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The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

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Authors: Patricia Jayshree Jacob, Mas Jaffri Masarudinb, Mohd Zobir Hussein, Raha Abdul Rahim

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Iron based ferromagnetic nanoparticles (IONP) and silver nanostructures (AgNP) have found a wide range of application in antimicrobial therapy, cell targeting, and environmental applications. As such, the design of well-defined monodisperse IONPs and AgNPs have become an essential tool in nanotechnology. Fabrication of these nanostructures using conventional methods is not environmentally conducive and weigh heavily on energy and outlays. Selected microorganisms possess the innate ability to reduce metallic ions in colloidal aqueous solution to generate nanoparticles. Hence, harnessing this potential is a way forward in constructing microbial nano-factories, capable of churning out high yields of well-defined IONP’s and AgNP's with physicochemical characteristics on par with the best synthetically produced nanostructures. In this paper, we report the isolation and characterization of bacterial strains isolated from the tropical marine and freshwater ecosystems of Malaysia that demonstrated facile and rapid generation of ferromagnetic nanoparticles and silver nanostructures when precursors such as FeCl₃.6H₂O and AgNO₃ were added to the cell-free bacterial lysate in colloidal solution. Characterization of these nanoparticles was carried out using FESEM, UV Spectrophotometer, XRD, DLS and FTIR. This aerobic bioprocess was carried out at ambient temperature and humidity and has the potential to be developed for environmental friendly, cost effective large scale production of IONP’s. A preliminary bioprocess study on the harvesting time, incubation temperature and pH was also carried out to determine pertinent abiotic parameters contributing to the optimal production of these nanostructures.

Keywords: iron oxide nanoparticles, silver nanoparticles, biosynthesis, aquatic bacteria

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Authors: Anza-Vhudziki Mboyi, Ilunga Kamika, Maggy Momba

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The aim of this study was to ascertain the survival limit and capability of commonly found wastewater protozoan (Aspidisca sp, Trachelophyllum sp, and Peranema sp) and bacterial (Bacillus licheniformis, Brevibacillus laterosporus, and Pseudomonas putida) species to remove COD while exposed to commercial nanomaterials under varying pH conditions. The experimental study was carried out in modified mixed liquor media adjusted to various pH levels (pH 2, 7 and 10), and a comparative study was performed to determine the difference between the cytotoxicity effects of commercial zinc oxide (nZnO) and silver (nAg) nanomaterials (NMs) on the target wastewater microbial communities using standard methods. The selected microbial communities were exposed to lethal concentrations ranging from 0.015 g/L to 40 g/L for nZnO and from 0.015 g/L to 2 g/L for nAg for a period of 5 days of incubation at 30°C (100 r/min). Compared with the absence of NMs in wastewater mixed liquor, the relevant environmental concentration ranging between 10 µg/L and 100 µg/L, for both nZnO and nAg caused no adverse effects, but the presence of 20 g of nZnO/L and 0.65 g of nAg/L significantly inhibited microbial growth. Statistical evidence showed that nAg was significantly more toxic compared to nZnO, but there was an insignificant difference in toxicity between microbial communities and pH variations. A significant decrease in the removal of COD by microbial populations was observed in the presence of NMs with a moderate correlation of r = 0.3 to r = 0.7 at all pH levels. It was evident that there was a physical interaction between commercial NMs and target wastewater microbial communities; although not quantitatively assessed, cell morphology and cell death were observed. Such phenomena suggest the high resilience of the microbial community, but it is the accumulation of NMs that will have adverse effects on the performance in terms of COD removal.

Keywords: bacteria, biological treatment, chemical oxygen demand (COD) and nanomaterials, consortium, pH, protozoan

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Authors: Okolie Pius Ifeanyi, Emerenini Emilymary Chima

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Aims: The study investigated the diversity and identities of Lactic Acid Bacteria (LAB) isolated from different fresh fruits using Molecular Nested PCR analysis and the efficacy of cell free supernatants from Lactic Acid Bacteria (LAB) isolated from fresh fruits for in vitro control of some tomato pathogens. Study Design: Nested PCR approach was used in this study employing universal 16S rRNA gene primers in the first round PCR and LAB specific Primers in the second round PCR with the view of generating specific Nested PCR products for the LAB diversity present in the samples. The inhibitory potentials of supernatant obtained from LAB isolates of fruits origin that were molecularly characterized were investigated against some tomato phytopathogens using agar-well method with the view to develop biological agents for some tomato disease causing organisms. Methodology: Gram positive, catalase negative strains of LAB were isolated from fresh fruits on Man Rogosa and Sharpe agar (Lab M) using streaking method. Isolates obtained were molecularly characterized by means of genomic DNA extraction kit (Norgen Biotek, Canada) method. Standard methods were used for Nested Polymerase Chain Reaction (PCR) amplification targeting the 16S rRNA gene using universal 16S rRNA gene and LAB specific primers, agarose gel electrophoresis, purification and sequencing of generated Nested PCR products (Macrogen Inc., USA). The partial sequences obtained were identified by blasting in the non-redundant nucleotide database of National Center for Biotechnology Information (NCBI). The antimicrobial activities of characterized LAB against some tomato phytopathogenic bacteria which include (Xanthomonas campestries, Erwinia caratovora, and Pseudomonas syringae) were obtained by using the agar well diffusion method. Results: The partial sequences obtained were deposited in the database of National Centre for Biotechnology Information (NCBI). Isolates were identified based upon the sequences as Weissella cibaria (4, 18.18%), Weissella confusa (3, 13.64%), Leuconostoc paramensenteroides (1, 4.55%), Lactobacillus plantarum (8, 36.36%), Lactobacillus paraplantarum (1, 4.55%) and Lactobacillus pentosus (1, 4.55%). The cell free supernatants of LAB from fresh fruits origin (Weissella cibaria, Weissella confusa, Leuconostoc paramensenteroides, Lactobacillus plantarum, Lactobacillus paraplantarum and Lactobacillus pentosus) can inhibits these bacteria by creating clear zones of inhibition around the wells containing cell free supernatants of the above mentioned strains of lactic acid bacteria. Conclusion: This study shows that potentially LAB can be quickly characterized by molecular methods to specie level by nested PCR analysis of the bacteria isolate genomic DNA using universal 16S rRNA primers and LAB specific primer. Tomato disease causing organisms can be most likely biologically controlled by using extracts from LAB. This finding will reduce the potential hazard from the use of chemical herbicides on plant.

Keywords: nested pcr, molecular characterization, 16s rRNA gene, lactic acid bacteria

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Authors: Vipin Kumar Verma, Neeta Sehgal, Om Prakash

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Cyprinus carpio has a wide spread occurrence in the lakes and rivers of Europe and Asia. Heavy losses in natural environment due to anthropogenic activities, including pollution as well as pathogenic diseases have landed this fish in IUCN red list of vulnerable species. The significance of a suitable diet in preserving the health status of fish is widely recognized. In present study, artificial feed supplemented with leaves of two weed plants, Eichhornia crassipes and Ricinus communis were evaluated for their role on the fish immune system. To achieve this objective fish were acclimatized to laboratory conditions (25 ± 1 °C; 12 L: 12D) for 10 days prior to start of experiment and divided into 4 groups: non-challenged (negative control= A), challenged [positive control (B) and experimental (C & D)]. Group A, B were fed with non-supplemented feed while group C & D were fed with feed supplemented with 5% Eichhornia crassipes and 5% Ricinus communis respectively. Supplemented feeds were evaluated for their effect on growth, health, immune system and disease resistance in fish when challenged with Vibrio harveyi. Fingerlings of C. carpio (weight, 2.0±0.5 g) were exposed with fresh overnight culture of V. harveyi through bath immunization (concentration 2 Χ 105) for 2 hours on 10 days interval for 40 days. The growth was monitored through increase in their relative weight. The rate of mortality due to bacterial infection as well as due to effect of feed was recorded accordingly. Immune response of fish was analyzed through differential leucocyte count, percentage phagocytosis and phagocytic index. The effect of V. harveyi on fish organs were examined through histo-pathological examination of internal organs like spleen, liver and kidney. The change in the immune response was also observed through gene expression analysis. The antioxidant potential of plant extracts was measured through DPPH and FRAP assay and amount of total phenols and flavonoids were calculates through biochemical analysis. The chemical composition of plant’s methanol extracts was determined by GC-MS analysis, which showed presence of various secondary metabolites and other compounds. Investigation revealed immuno-modulatory effect of plants, when supplemented with the artificial feed of fish.

Keywords: immuno-modulation, gc-ms, Cyprinus carpio, Eichhornia crassipes, Ricinus communis

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Authors: Katerina Balounova, Jiri Pacha, Peter Ergang, Martin Vodicka, Pavlina Kvapilova

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MicroRNAs are small non-coding RNAs involved in a wide range of physiological processes. Post-transcriptional regulation of gene expression by microRNAs gives the organism a further level of control of the gene-expression program and the disruption of this microRNA regulatory mechanism seems to increase the risk of various pathophysiological conditions including tumorigenesis. To the present day, microRNAs were shown to participate in the mayor signalization pathways leading to tumorigenesis, including proliferation, cell cycle, apoptosis and metastasis formation. In addition, microRNAs have been found to play important roles in the generation and maintenance of circadian clock. These clocks generate circadian rhythms, which participate in a number of regulatory pathways. Disruption of the circadian signals seems to be associated with the development and the progression of tumours including colorectal cancer. We investigated therefore whether the diurnal profiles of miRNAs linked to tumorigenesis and regulation of circadian clock are changed during tumorigenesis. Based on published data we chose 10 microRNAs linked to tumorigenesis or circadian clock (let-7b-5p, miR 1 3p, miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p, miR 29a 3p, miR 34a 5p and miR 93 5p) and compared their 24-hr expression profiles in healthy and in chemically induces primary colorectal tumours of 52week-old mice. Using RT-qPCR we proved circadian rhythmicity in let-7b-5p, miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p, miR 29a 3p and miR 93 5p in healthy colon but not in tumours. The acrophases of miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p and miR 93 5p were reached around CT 24, the acrophases of let-7b-5p and miR-29a-3p were slightly shifted and reached around CT 21. In summary, our results show that circadian regulation of some colonic microRNAs is greatly affected by neoplastic transformation.

Keywords: circadian rhythm, colon, colorectal cancer, microRNA, tumorigenesis

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Salina Saddick, Mohamed Afifi, Osama Abuznadah

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This study was carried out to determine the median lethal concentrations (LC50) of Zinc nanoparticles (ZnNPs) on Oreochromis niloticus and Tilapia zillii. The biochemical and molecular potential effects of ZnNPs (500 and 2000 μg L−1) on the antioxidant system in the brain tissue of O. niloticus and T. zillii were investigated. Four hundred fish were used for acute and sub-acute studies. ZnNP LC50 concentrations were investigated in O. niloticus and T. zillii. The effect of 500 and 2000 μg L−1 ZnNPs on brain antioxidants of O. niloticus and T. zillii was investigated. The result indicated that 69 h LC50 was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. Fish exposed to 500 μg L−1 ZnNPs showed a significant increase in reduced glutathione (GSH), total glutathione (tGSH) levels, superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) activity and gene expression. On the contrary, malondialdehyde (MDA) levels significantly decreased. Meanwhile, fish exposed to 2000 μg L−1 ZnNPs showed a significant decrease of GSH, tGSH levels, SOD, CAT, GR, GPx and GST activity and gene expression. On the contrary, MDA levels significantly increased. It was concluded that, the 96 h LC50 of ZnNPs was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. ZnNPs in exposure concentrations of 2000 μg/L induced a deleterious effect on the brain antioxidant system of O. nilotica and T. zillii. In contrast, ZnNPs in exposure concentrations of 500 μg L−1 produced an inductive effect on the brain antioxidant system of O. nilotica and T. zillii.

Keywords: ZnNPs, LC50, antioxidants, O. nilotica

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Seyed Davar Siadat, Samira Tarashi, Abolfazl Fateh, Arfa Moshiri

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Background: The global health issue of tuberculosis (TB) still affects patients in every country. TB control may not be as effective as it should be, especially when resistant strains are involved. In this regard, mycobacterial MTases play a major role in tuberculosis, but the mechanisms underlying their function have yet to be fully deciphered. Methods: Five resistant isolates of M.tb were accumulated. As a reference strain, M.tb H37Rv (ATCC 27249) was used. For this analysis, seven putative mycobacterial MTase genes (Rv0645c, Rv1694, Rv2966c, Rv3919c, Rv2756c, Rv1988, and Rv3263), as well as Rv1392 as SAM synthase, were selected. Comparing mutations and expression levels of MTases in different strains was accomplished by PCR-sequencing and qRT-PCR. The relative expression levels of these genes were calculated using the 2 -ΔΔCt method. Results: The Rv3919c gene (T to G in codon 341) and Rv1392 gene (G to A in codon 97) were the only mutations found in the INHR strain. In all sensitive and resistant isolates, Rv0645c, Rv3263, Rv2756c, and Rv2966c were overexpressed. However, the expression of Rv1988 and Rv3919c decreased in the sensitive strains, whereas the expression of Rv1694 increased. There was also a decreased expression of Rv1392 in the INHR isolate. Conclusion: The presence of mycobacterial MTases as well as resistance to antibiotics were found to be correlated in M.tb strains. Undoubtedly, there are some MTases that are associated with the virulence process. It is necessary to conduct additional studies to fully explore the impact of mycobacterial MTases within specific strains of M.tb to develop novel diagnostic and treatment strategies.

Keywords: mycobacterium tuberculosis, drug resistance, methyltransferases, s-adenosylmethionine

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Authors: Mukta Singh, Ratan Kumar Saha, Himadri Saha, Paramveer Singh

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The present study evaluated the effect of sub-lethal doses of antifungal drug miconazole nitrate (MCZ) on immunological responses including immune-related gene expression and its role as a prophylactic drug against S. parasitica in Labeo rohita fingerlings. Fish were fed with sub lethal doses of MCZ i.e., T1- 6.30 mg MCZ kgBW⁻¹, T2- 12.61 mg MCZ kgBW⁻¹ and T3- 25.22 mg MCZ kgBW⁻¹ and sampling was done at different time intervals for 240 h. Immunological parameters viz. lysozyme activity, oxygen radical production and plasma anti-protease activity showed significant enhancement (p < 0.05) in fish fed with T2 and T3 doses. Significant reduction in plasma protein content was observed in all the dietary groups as compared to control. Expression of immune-relevant genes like TLR-22 and β2-M showed significantly higher expression at six h and 24 h of sampling in both liver and head-kidney. However, these genes showed a down-regulation after 120 h of sampling in both the tissues. Preventive efficacy study showed that single dose of MCZ provides protection against oomycetes up to the fourth day of infection. Significantly higher mortality was observed in control diet-fed fish as compared to fish fed with MCZ medicated diet. Thus, from the study, it can be concluded that the MCZ can act as a potent antifungal agent for preventing oomycetes infection as well as to enhance the immune response.

Keywords: antifungal, immune gene, immunological, miconazole nitrate, prophylactic

Procedia PDF Downloads 246