Search results for: genetic profiles

Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: Arun K. Yadav, Adam J. Carroll, Gonzalo M. Estavillo, Greg J. Rebetzke, Barry J. Pogson

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Water limits crop productivity, so selecting for minimal yield-gap in drier environments is critical to mitigate against climate change and land-use pressures. To date, no markers measured in glasshouses have been reported to predict field-based drought tolerance. In the field, the best measure of drought tolerance is yield-gap; but this requires multisite trials that are an order of magnitude more resource intensive and can be impacted by weather variation. We investigated the responses of relative water content (RWC), stomatal conductance (gs), chlorophyll content and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites and Yield gap-based Drought Tolerance (YDT): the ratio of yield in water-limited versus well-watered conditions across 24 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2 = 0.85, p < 8E-6) and RWC under field drought (r2 = 0.77, p < 0.05). Multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: serine, asparagine, methionine and lysine (R2 = 0.98; p < 0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for the selection of wheat cultivars with high YDT in the field.

Keywords: drought stress, grain yield, metabolomics, stomatal conductance, wheat

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Authors: Bedilu Tafesse

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Conservation of crop genetic resources presents a challenge of identifying specific determinants driving maintenance of diversity at farm and agroecosystems. The objectives of this study were to identify socioeconomic, market and agroecological determinants of farmers’ maintenance of wheat diversity at the household level and derive implications for policies in designing on-farm conservation programs. We assess wheat diversity at farm level using household survey data. A household decision making model is conceptualized using microeconomic theory to assess and identify factors influencing on-farm rice diversity. The model is then tested econometrically by using various factors affecting farmers’ variety choice and diversity decisions. The findings show that household-specific socioeconomic, agroecological and market factors are important in determining on-farm wheat diversity. The significant variables in explaining richness and evenness of wheat diversity include distance to the nearest market, subsistence ratio, modern variety sold, land types and adult labour working in agriculture. The statistical signs of the factors determining wheat diversity are consistent in explaining the richness, dominance and evenness among rice varieties. Finally, the study implies that the cost-effective means of promoting and sustaining on-farm conservation programmes is to target them in market isolated geographic locations of high crop diversity where farm households have more heterogeneity of agroecological conditions and more active family adult labour working on-farm.

Keywords: diversity indices, dominance, evenness, on-farm conservation, wheat diversity, richness

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Authors: Javad Jamali Khouei, Mohammadreza Khoshravan

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Considering that application of functionally graded material is increasing in most industries, it seems necessary to present a methodology for designing optimal profile of structures such as plate under mechanical loading which is highly consumed in industries. Therefore, volume fraction variation profile of functionally graded circular plate which has been considered two-directional is optimized so that stress of structure is minimized. For this purpose, equilibrium equations of two-directional functionally graded circular plate are solved by applying semi analytical-numerical method under mechanical loading and support conditions. By solving equilibrium equations, deflections and stresses are obtained in terms of control variables of volume fraction variation profile. As a result, the problem formula can be defined as an optimization problem by aiming at minimization of critical von-mises stress under constraints of deflections, stress and a physical constraint relating to structure of material. Then, the related problem can be solved with help of one of the metaheuristic algorithms such as genetic algorithm. Results of optimization for the applied model under constraints and loadings and boundary conditions show that functionally graded plate should be graded only in radial direction and there is no need for volume fraction variation of the constituent particles in thickness direction. For validating results, optimal values of the obtained design variables are graphically evaluated.

Keywords: two-directional functionally graded material, single objective optimization, semi analytical-numerical solution, genetic algorithm, graphical solution with contour

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Authors: Yude Wu

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Mongolia, grappling with significant socio-economic challenges, faces pressing issues of inequality and poverty, as evidenced by a high Gini coefficient and the highest poverty rate among the top 20 largest Asian countries. Despite government efforts, Mongolia's poverty rate experienced only a slight reduction from 29.6 percent in 2016 to 27.8 percent in 2020. PEER countries, such as South Africa, Botswana, Kazakhstan, and Peru, share characteristics with Mongolia, including reliance on the mining industry and classification as lower middle-income countries. Successful transitions of these countries to upper middle-income status between 1994 and the 2010s provide valuable insights. Drawing on secondary analyses of existing research and PEER country profiles, the study evaluates past policies, identifies gaps in current approaches, and proposes recommendations to combat poverty sustainably. The hypothesis includes a reliance on the mining industry and a transition from lower to upper middle-income status. Policies from these countries, such as the GEAR policy in South Africa and economic diversification in Botswana, offer insights into Mongolia's development. This essay aims to illuminate the multidimensional nature of underdevelopment in Mongolia through a secondary analysis of existing research and PEER country profiles, evaluating past policies, identifying gaps in current approaches, and providing recommendations for sustainable progress. Drawing inspiration from PEER countries, Mongolia can implement policies such as economic diversification to reduce vulnerability and create stable job opportunities. Emphasis on infrastructure, human capital, and strategic partnerships for Foreign Direct Investment (FDI) aligns with successful strategies implemented by PEER countries, providing a roadmap for Mongolia's development objectives.

Keywords: inequality, PEER countries, comparative analysis, nomadic animal husbandry, sustainable growth

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Authors: Aneal Khan, Elleine Allapitan, Desmond Koo, Katherine-Ann Piedalue, Shaneel Pathak, Utkarsh Subnis

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Background: Disease management of metabolic, genetic disorders is long-term and can be cumbersome to patients and caregivers. Patient-Reported Outcome Measures (PROMs) have been a useful tool in capturing patient perspectives to help enhance treatment compliance and engagement with health care providers, reduce utilization of emergency services, and increase satisfaction with their treatment choices. Currently, however, PROMs are collected during infrequent and decontextualized clinic visits, which makes translation of patient experiences challenging over time. The GRIT study aims to evaluate a digital health journal application called Zamplo that provides a personalized health diary to record self-reported health outcomes accurately and efficiently in patients with metabolic, genetic disorders. Methods: This is a randomized controlled trial (RCT) (1:1) that assesses the efficacy of Zamplo to increase patient activation (primary outcome), improve healthcare satisfaction and confidence to manage medications (secondary outcomes), and reduce costs to the healthcare system (exploratory). Using standardized online surveys, assessments will be collected at baseline, 1 month, 3 months, 6 months, and 12 months. Outcomes will be compared between patients who were given access to the application versus those with no access. Results: Seventy-seven patients were recruited as of November 30, 2021. Recruitment for the study commenced in November 2020 with a target of n=150 patients. The accrual rate was 50% from those eligible and invited for the study, with the majority of patients having Fabry disease (n=48) and the remaining having Pompe disease and mitochondrial disease. Real-time clinical responses, such as pain, are being measured and correlated to disease-modifying therapies, supportive treatments like pain medications, and lifestyle interventions. Engagement with the application, along with compliance metrics of surveys and journal entries, are being analyzed. An interim analysis of the engagement data along with preliminary findings from this pilot RCT, and qualitative patient feedback will be presented. Conclusions: The digital self-care journal provides a unique approach to disease management, allowing patients direct access to their progress and actively participating in their care. Findings from the study can help serve the virtual care needs of patients with metabolic, genetic disorders in North America and the world over.

Keywords: eHealth, mobile health, rare disease, patient outcomes, quality of life (QoL), pain, Fabry disease, Pompe disease

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Authors: Thobela Conco, Sheena Kumari, Chika Nnadozie, Mahmoud Nasr, Thor A. Stenström, Mushal Ali, Arshad Ismail, Faizal Bux

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The discharge of antibiotics and its residues into the wastewater treatment plants (WWTP’s) create a conducive environment for the development of antibiotic resistant pathogens. This presents a risk of potential dissemination of antibiotic resistant pathogens and antibiotic resistance genes into the environment. It is, therefore, necessary to study the level of antibiotic resistance genes (ARG’s) among bacterial pathogens that proliferate in biological wastewater treatment systems. In the current study, metagenomic and meta-transcriptomic sequences of samples collected from the influents, secondary effluents and post chlorinated effluents of three wastewater treatment plants treating domestic and hospital effluents in Durban, South Africa, were analyzed for profiling of ARG’s among bacterial pathogens. Results show that a variety of ARG’s, mostly, aminoglycoside, β-lactamases, tetracycline and sulfonamide resistance genes were harbored by diverse bacterial genera found at different stages of treatment. A significant variation in diversity of pathogen and ARGs between the treatment plant was observed; however, treated final effluent samples from all three plants showed a significant reduction in bacterial pathogens and detected ARG’s. Both pre- and post-chlorinated samples showed the presence of mobile genetic elements (MGE’s), indicating the inefficiency of chlorination to remove of ARG’s integrated with MGE’s. In conclusion, the study showed the wastewater treatment plant efficiently caused the reduction and removal of certain ARG’s, even though the initial focus was the removal of biological nutrients.

Keywords: antibiotic resistance, mobile genetic elements, wastewater, wastewater treatment plants

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Authors: R. Raudonis, L. Raudonė, V. Janulis, P. Viškelis

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Pharmacological and clinical studies demonstrated that phenolic compounds particularly flavonoids and phenolic acids are responsible for a wide spectrum of therapeutic activities. Flavonoids and phenolic acids are regarded as natural antioxidants that play an important role in protecting cells from oxidative stress. Qualitatively prepared dry extracts possess high stability and concentration of bio active compounds, facility of standardization and quality control. The aim of this work was to determine the phenolic and antioxidant profiles of Hippophaë rhamnoides L., Betula pendula Roth., Tilia cordata Mill., Sorbus aucuparia L. leaves dry extracts and to identify markers of antioxidant activity. Extracts were analyzed using high-performance liquid chromatography (HPLC) with FRAP post-column assay. Dry extracts are versatile forms possessing wide area of applications, final product ensure consistent phytochemical and functional properties. Seven flavonoids: rutin, hyperoside, isorhamnetin 3-O-rutinoside, isorhamnetin 3-O-glucoside, quercetin, kaempferol, isorhamnetin were identified in dry extract of Hippophaë rhamnoides L. leaves. Predominant compounds were flavonol glycosides which were chosen as markers for quantitative control of dry extracts. Chlorogenic acid, hyperoside, rutin, quercetin, isorhamnetin were prevailing compounds in Betula pendula Roth. leaves extract, whereas strongest ferric reducing activity was determined for chlorogenic acid and hyperoside. Notable amounts of protocatechuic acid and flavonol glycosides, rutin, hyperoside, quercitrin, isoquercitrin were identified in the chromatographic profile of Tilia cordata Mill. Neochlorogenic and chlorogenic acids were significantly dominant compounds in antioxidant profile in dry extract of Sorbus aucuparia L. leaves. Predominant compounds of antioxidant profiles could be proposed as functional markers of quality of phenolic rich raw materials. Dry extracts could be further used for manufacturing of pharmaceutical and nutraceuticals.

Keywords: dry extract, FRAP, antioxidant activity, phenolic

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Authors: Dace Grauda, Gunta Cekstere, Inta Belogrudova, Andis Karlsons, Isaak Rashal

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Trifolium repens L. (white or Dutch clover) is a perennial herb, belongs to legume family (Leguminosae Juss.), spread extensively by stolons and seeds. The species is cultivated worldwide and was naturalized in many countries in meadows, yards, gardens, along roads and streets etc., especially in temperate regions. It is widespread also in grasslands throughout Riga, the capital of Latvia. The goal of this study was to investigate genetic structure of white clover population in Riga and to evaluate influence of different salt concentration on plants. For this purpose universal retrotranspozone based IRAP (Inter-Retrotransposon Amplified Polymorphism) method was used. The plant material was collected in different regions of Riga and in several urban areas of Latvia. Plant DNA was isolated from in silicogel dried leaves of using 1% CTAB (cetyltrimet-ammonium bromide) buffer DNA extraction procedure. Genetic structure of city population and wild populations were compared. Soil salinization is an important issue associated with low water resources and highly urbanized areas in aride and semi-aride climate conditions, as well as de-icing salt application to prevent ice formation on roads in winter. The T. repens variety ‘Daile’ (form giganteum), one of the often used component of urban greeneries, was studied in this investigation. Plants were grown from seeds and cultivated in the light conditions (18-25 C, 16h/8h of day/night, light intensity 3000 lx) in plastic pots (200 ml), filled with commercial neutralized (pH 5.9 ± 0.3) peat substrate with mineral nutrients. To analyse the impact of increased soil salinity treatments with gradually rising NaCl (0; 20; 40; 60; 80; 100 mM) levels were arranged. Plants were watered when necessary with deionised water to provide optimum substrate moisture 60-70%. The experiment was terminated six weeks after establishment. For analysis of mineral nutrients, dry plant material (above ground part and roots) was used. Decrease of Na content can be significant under elevated salinity till 20 mM NaCl. High NaCl concentrations in the substrate increase Na, Cl, Cu, Fe, and Mn accumulation, but reduce S, Mg, K content in the plant above ground parts. Abiotic stresses generally changes the levels of DNA metilation. Several candidate gene for salt tolerance will be analysed for DNA metilation level using Pyromark-Q24 advanced.

Keywords: DNA metilation, IRAP, soil salinization, white clover

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Authors: Sampo Tukiainen, Jukka Mattila, Niina Erkama, Erkki Ormala

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During the past decade, calls for more holistic and integrative organizational innovation research have been increasingly voiced. On the one hand, from the theoretical perspective, the reason for this has been the tendency in contemporary innovation studies to focus on disciplinary subfields, often leading to challenges in integrating theories in meaningful ways. For example, we find that during the past three decades the innovation research has evolved into an academic field consisting of several independent research streams, such as studies on organizational learning, project management, and top management teams, to name but a few. The innovation research has also proliferated according to different dimensions of innovation, such as sources, drivers, forms, and the nature of innovation. On the other hand, from the practical perspective the rationale has been the need to develop understanding of the solving of complex, interdisciplinary issues and problems in contemporary and future societies and organizations. Therefore, for advancing theorizing, as well as the practical applicability of organizational innovation research, we acknowledge the need for more integrative and holistic perspectives and approaches. We contribute to addressing this challenge by developing a ‘box transcendent’ perspective to examine interlinkages in and across four key dimensions of organizational innovation processes, which traditionally have been studied in separate research streams. Building on an in-depth, qualitative analysis of 123 interviews of CTOs (or equivalent) and CEOs in top innovative Finnish companies as well as three in-depth case studies, both as part of an EU-level interview study of more than 700 companies, we specify interlinkages in and between i) strategic management, ii) innovation management, iii) implementation and organization, and iv) commercialization, in innovation processes. We contribute to the existing innovation research in multiple ways. Firstly, we develop a cross-dimensional, ‘box transcendent’ conceptual model at the level of organizational innovation process. Secondly, this modeling enables us to extend existing theorizing by allowing us to distinguish specific cross-dimensional innovation ‘profiles’ in two different company categories: large multinational corporations and SMEs. Finally, from the more practical perspective, we consider the implications of such innovation ‘profiles’ for the societal and institutional, policy-making development.

Keywords: holistic research, innovation management, innovation studies, organizational innovation

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Authors: Hamna Choudhary

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Background: This clinical case report follows the orthodontic journey of a teenage girl being treated in the Oxfordshire Community Dental Service. She presents with a rare genetic disorder – Moebius syndrome – characterised by unilateral or bilateral facial (CN VII) and abducens (CN VI) nerve palsy. This report seeks to educate Dental professionals on the impact of Moebius syndrome on Dental treatment, and how to make reasonable adjustments to make orthodontic care accessible to these patients. Methodology: Moebius syndrome is a very rare genetic disorder. Across the Oxfordshire Community Dental Service, only two patients with this condition have been identified who are undergoing orthodontic treatment. One of these patients was selected and observed, while the orthodontist (Heather Nevard) was providing orthodontic treatment with fixed appliances. The patient is undergoing treatment to correct her class II division 2 incisor relationship complicated by buccally excluded, transposed maxillary canines. Conclusions: Specific oral presentations of Moebius syndrome include microstomia, micrognathia, tongue malformation, high or cleft palate, bifid uvula and Dental malocclusion. Orthodontics plays a major role in managing and correcting many of these conditions. This emphasises the importance for Dental professionals to be informed on the condition and highlights the need for Dental input in multidisciplinary teams responsible for the care of these patients. Receiving corrective treatment has a significant impact on an individual’s quality of life. In this case, the patient felt much more confident in herself, and having aligned teeth will allow her to better maintain a healthy dentition throughout life. By understanding and educating oneself on Moebius syndrome, one is able to better cater to patient needs and make orthodontic treatment accessible.

Keywords: dentistry, facial palsy, moebius syndrome, orthodontics

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Authors: M. A. Talha, M. Osman Gani, M. Ferdows

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This paper focuses on the study of two dimensional magnetohydrodynamic (MHD) steady incompressible viscous Williamson nanofluid with exponential internal heat generation containing gyrotactic microorganism over a stretching sheet. The governing equations and auxiliary conditions are reduced to a set of non-linear coupled differential equations with the appropriate boundary conditions using similarity transformation. The transformed equations are solved numerically through spectral relaxation method. The influences of various parameters such as Williamson parameter γ, power constant λ, Prandtl number P_r, magnetic field parameter M, Peclet number P_e, Lewis number Le, Bioconvection Lewis number Lb, Brownian motion parameter Nb, thermophoresis parameter Nt, and bioconvection constant σ are studied to obtain the momentum, heat, mass and microorganism distributions. Moment, heat, mass and gyrotactic microorganism profiles are explored through graphs and tables. We computed the heat transfer rate, mass flux rate and the density number of the motile microorganism near the surface. Our numerical results are in better agreement in comparison with existing calculations. The Residual error of our obtained solutions is determined in order to see the convergence rate against iteration. Faster convergence is achieved when internal heat generation is absent. The effect of magnetic parameter M decreases the momentum boundary layer thickness but increases the thermal boundary layer thickness. It is apparent that bioconvection Lewis number and bioconvection parameter has a pronounced effect on microorganism boundary. Increasing brownian motion parameter and Lewis number decreases the thermal boundary layer. Furthermore, magnetic field parameter and thermophoresis parameter has an induced effect on concentration profiles.

Keywords: convection flow, similarity, numerical analysis, spectral method, Williamson nanofluid, internal heat generation

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Authors: Wanchalerm Patanacharoenwong, Panaya Sudta, Prachya Bumrungkun

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The paper focuses on the development of a system that combines Internet of Things (IoT) technologies and deep learning algorithms for anomaly detection in residential Electric Vehicle (EV) charging in smart cities. With the increasing number of EVs, ensuring efficient and reliable charging systems has become crucial. The aim of this research is to develop an integrated IoT and deep learning system for detecting anomalies in residential EV charging and enhancing EV load profiling and event detection in smart cities. This approach utilizes IoT devices equipped with infrared cameras to collect thermal images and household EV charging profiles from the database of Thailand utility, subsequently transmitting this data to a cloud database for comprehensive analysis. The methodology includes the use of advanced deep learning techniques such as Recurrent Neural Networks (RNN) and Long Short-Term Memory (LSTM) algorithms. IoT devices equipped with infrared cameras are used to collect thermal images and EV charging profiles. The data is transmitted to a cloud database for comprehensive analysis. The researchers also utilize feature-based Gaussian mixture models for EV load profiling and event detection. Moreover, the research findings demonstrate the effectiveness of the developed system in detecting anomalies and critical profiles in EV charging behavior. The system provides timely alarms to users regarding potential issues and categorizes the severity of detected problems based on a health index for each charging device. The system also outperforms existing models in event detection accuracy. This research contributes to the field by showcasing the potential of integrating IoT and deep learning techniques in managing residential EV charging in smart cities. The system ensures operational safety and efficiency while also promoting sustainable energy management. The data is collected using IoT devices equipped with infrared cameras and is stored in a cloud database for analysis. The collected data is then analyzed using RNN, LSTM, and feature-based Gaussian mixture models. The approach includes both EV load profiling and event detection, utilizing a feature-based Gaussian mixture model. This comprehensive method aids in identifying unique power consumption patterns among EV owners and outperforms existing models in event detection accuracy. In summary, the research concludes that integrating IoT and deep learning techniques can effectively detect anomalies in residential EV charging and enhance EV load profiling and event detection accuracy. The developed system ensures operational safety and efficiency, contributing to sustainable energy management in smart cities.

Keywords: cloud computing framework, recurrent neural networks, long short-term memory, Iot, EV charging, smart grids

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Authors: Mohamed Driouich, Kamal Gueraoui, Mohamed Sammouda

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The main objective of this work is to establish a numerical code for studying the flow of molten polymers in deformable pipes. Using an iterative numerical method based on finite differences, we determine the profiles of the fluid velocity, the temperature and the apparent viscosity of the fluid. The numerical code presented can also be applied to other industrial applications.

Keywords: numerical code, molten polymers, deformable pipes, finite differences

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Authors: Leila Noori, Rosario Barone, Francesca Rappa, Antonella Marino Gammazza, Alessandra Maria Vitale, Giuseppe Donato Mangano, Giusy Sentiero, Filippo Macaluso, Kathryn H. Myburgh, Francesco Cappello, Federica Scalia

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The neuromuscular system controls, directs, and allows movement of the body through the action of neural circuits, which include motor neurons, sensory neurons, and skeletal muscle fibers. Protein homeostasis of the involved cytotypes appears crucial to maintain the correct and prolonged functions of the neuromuscular system, and both neuronal cells and skeletal muscle fibers express significant quantities of protein chaperones, the molecular machinery responsible to maintain the protein turnover. Genetic mutations or defective post-translational modifications of molecular chaperones (i.e., genetic or acquired chaperonopathies) may lead to neuromuscular disorders called as neurochaperonopathies. The limited knowledge of the effects of the defective chaperones on skeletal muscle fibers and neurons impedes the progression of therapeutic approaches. A distinct genetic variation of CCT5 gene encoding for the subunit 5 of the chaperonin CCT (Chaperonin Containing TCP1; also known as TRiC, TCP1 Ring Complex) was recently described associated with severe distal motor neuropathy by our team. In this study, we investigated the histopathological abnormalities of the skeletal muscle biopsy of the pediatric patient affected by the mutation Leu224Val in the CCT5 subunit. We provide molecular and structural features of the diseased skeletal muscle tissue that we believe may be useful to identify undiagnosed cases of this rare genetic disorder. We investigated the histological abnormalities of the affected tissue via hematoxylin and eosin staining. Then we used immunofluorescence and qPCR techniques to explore the expression and distribution of CCT5 in diseased and healthy skeletal muscle tissue. Immunofluorescence and immunohistochemistry assays were performed to study the sarcomeric and structural proteins of skeletal muscle, including actin, myosin, tubulin, troponin-T, telethonin, and titin. We performed Western blot to examine the protein expression of CCT5 and some heat shock proteins, Hsp90, Hsp60, Hsp27, and α-B crystallin, along with the main client proteins of the CCT5, actin, and tubulin. Our findings revealed muscular atrophy, abnormal morphology, and different sizes of muscle fibers in affected tissue. The swollen nuclei and wide interfiber spaces were seen. Expression of CCT5 had been decreased and showed a different distribution pattern in the affected tissue. Altered expression, distribution, and bandage pattern were detected by confocal microscopy for the interested muscular proteins in tissue from the patient compared to the healthy control. Protein levels of the studied Hsps normally located at the Z-disk were reduced. Western blot results showed increased levels of the actin and tubulin proteins in the diseased skeletal muscle biopsy compared to healthy tissue. Chaperones must be expressed at high levels in skeletal muscle to counteract various stressors such as mechanical, oxidative, and thermal crises; therefore, it seems relevant that defects of molecular chaperones may result in damaged skeletal muscle fibers. So far, several chaperones or cochaperones involved in neuromuscular disorders have been defined. Our study shows that alteration of the CCT5 subunit is associated with the damaged structure of skeletal muscle fibers and alterations of chaperone system components and paves the way to explore possible alternative substrates of chaperonin CCT. However, further studies are underway to investigate the CCT mechanisms of action to design applicable therapeutic strategies.

Keywords: molecular chaperones, neurochaperonopathy, neuromuscular system, protein homeostasis

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Authors: A. Berraf-Tebbal, Z. Bouznad, , A.J.L. Phillips

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Phaeomoniella is a fungus genus in the mitosporic ascomycota which includes Phaeomoniella chlamydospora specie associated with two declining diseases on grapevine (Vitis vinifera) namely Petri disease and esca. Recent studies have shown that several Phaeomoniella species also cause disease on many other woody crops, such as forest trees and woody ornamentals. Two new species, Phaeomoniella zymoides and Phaeomoniella pinifoliorum H.B. Lee, J.Y. Park, R.C. Summerbell et H.S. Jung, were isolated from the needle surface of Pinus densiflora Sieb. et Zucc. in Korea. The identification of species in Phaeomoniella genus can be a difficult task if based solely on morphological and cultural characters. In this respect, the application of molecular methods, particularly PCR-based techniques, may provide an important contribution. MSP-PCR (microsatellite primed-PCR) fingerprinting has proven useful in the molecular typing of fungal strains. The high discriminatory potential of this method is particularly useful when dealing with closely related or cryptic species. In the present study, the application of PCR fingerprinting was performed using the micro satellite primer M13 for the purpose of species identification and strain typing of 84 Phaeomoniella -like isolates collected from grapevines with typical symptoms of dieback. The bands produced by MSP-PCR profiles divided the strains into 3 clusters and 5 singletons with a reproducibility level of 80%. Representative isolates from each group and, when possible, isolates from Eutypa dieback and esca symptoms were selected for sequencing of the ITS region. The ITS sequences for the 16 isolates selected from the MSP-PCR profiles were combined and aligned with sequences of 18 isolates retrieved from GenBank, representing a selection of all known Phaeomoniella species. DNA sequences were compared with those available in GenBank using Neighbor-joining (NJ) and Maximum-parsimony (MP) analyses. The phylogenetic trees of the ITS region revealed that the Phaeomoniella isolates clustered with Phaeomoniella chlamydospora reference sequences with a bootstrap support of 100 %. The complexity of the pathosystems vine-trunk diseases shows clearly the need to identify unambiguously the fungal component in order to allow a better understanding of the etiology of these diseases and justify the establishment of control strategies against these fungal agents.

Keywords: Genotyping, MSP-PCR, ITS, phylogeny, trunk diseases

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Authors: Rachael Bentley, Callahan Gergen, Brodie Thiede

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Roadways have a significant impact on the environment in so far as they function as barriers to wildlife movement, both through road mortality and through resultant road avoidance. Roads have an im-mense presence worldwide, and it is predicted to increase substantially in the next thirty years. As roadways become even more common, it is important to consider their environmental impact, and to mitigate the negative effects which they have on wildlife and wildlife mobility. In a thorough analysis of several related studies, a common conclusion was that roads cause habitat fragmentation, which can lead split populations to evolve differently, for better or for worse. Though some populations adapted positively to roadways, becoming more resistant to road mortality, and more tolerant to noise and chemical contamination, many others experienced maladaptation, either due to chemical contamination in and around their environment, or because of genetic mutations from inbreeding when their population was fragmented too substantially to support a large enough group for healthy genetic exchange. Large mammals were especially susceptible to maladaptation from inbreed-ing, as they require larger areas to roam and therefore require even more space to sustain a healthy population. Regardless of whether a species evolved positively or negatively as a result of their proximity to a road, animals tended to avoid roads, making the genetic diversity from habitat fragmentation an exceedingly prevalent issue in the larger discussion of road ecology. Additionally, the consideration of solu-tions, such as overpasses and underpasses, is crucial to ensuring the long term survival of many wildlife populations. In studies addressing the effectiveness of overpasses and underpasses, it seemed as though animals adjusted well to these sorts of solutions, but strategic place-ment, as well as proper sizing, proper height, shelter from road noise, and other considerations were important in construction. When an underpass or overpass was well-built and well-shielded from human activity, animals’ usage of the structure increased significantly throughout its first five years, thus reconnecting previously divided populations. Still, these structures are costly and they are often unable to fully address certain issues such as light, noise, and contaminants from vehicles. Therefore, the need for further discussion of new, crea-tive solutions remains paramount. Roads are one of the most consistent and prominent features of today’s landscape, but their environmental impacts are largely overlooked. While roads are useful for connecting people, they divide landscapes and animal habitats. Therefore, further research and investment in possible solutions is necessary to mitigate the negative effects which roads have on wildlife mobility and to pre-vent issues from resultant habitat fragmentation.

Keywords: fences, habitat fragmentation, roadways, wildlife mobility

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Authors: Bajraktarevic Adnan, Djukic Branka, Sporisevic Lutvo, Krdzalic Zecevic Belma, Uzicanin Sajra, Hadzimuratovic Admir, Hadzimuratovic Hadzipasic Emina, Abduzaimovic Alisa, Kustric Amer, Suljevic Ismet, Serafi Ismail, Tahmiscija Indira, Khatib Hakam, Semic Jusufagic Aida, Haas Helmut, Vladicic Aleksandra, Aplenc Richard, Kadic Deovic Aida

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Introduction: Joubert syndrome has an autosomal recessive pattern of inheritance. It is referred as the brain malfunctioning and caused due to the underdevelopment of the cerebellar vermis. Associated conditions involving the eye, the kidney, and ocular disease are well described. Aims: Research helps us better understand this diseases, Joubert syndrome and can lead to advances in diagnosis and treatment. Methods: Different several conditions have been described in which the molar tooth sign and characteristics of Joubert syndrome in ten different places in the world. Carrier testing and diagnosis are available if one of these gene mutations has been identified in an affected family member. Results: Authors have described eleven cases during twenty years of Joubert syndrome. It is a clinically and genetically heterogeneous group of disorders characterized by hypoplasia of the cerebellar vermis with the characteristic neuroradiologic molar tooth sign, and accompanying neurologic symptoms, including dysregulation of breathing pattern and developmental delay. We made confirmation of diagnosis in twin sisters with Joubert syndrome with renal anomalies. Ocular symptoms have existed in seven cases (63.64%) from total eleven. Eleven cases were different sex, five boys (45.45%) and six girls (54.44%). Conclusions: Joubert syndrome is inherited as an autosomal recessive genetic disorder with several features of the disease.

Keywords: Joubert syndrome, cerebellooculorenal syndrome, autosomal recessive genetic disorder (ARGD), children

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Authors: Kristina Amaleviciute, Ieva Jokubauskaite, Alvyra Slepetiene, Jonas Volungevicius, Inga Liaudanskiene

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The main task of this research was to investigate the chemical composition of the differently used soil in profiles. To identify the differences in the soil were investigated organic carbon (SOC) and its fractional composition: dissolved organic carbon (DOC), mobile humic acids (MHA) and C to N ratio of natural and anthropogenically affected Luvisols. Research object: natural and anthropogenically affected Luvisol, Akademija, Kedainiai, distr. Lithuania. Chemical analyses were carried out at the Chemical Research Laboratory of Institute of Agriculture, LAMMC. Soil samples for chemical analyses were taken from the genetics soil horizons. SOC was determined by the Tyurin method modified by Nikitin, measuring with spectrometer Cary 50 (VARIAN) in 590 nm wavelength using glucose standards. For mobile humic acids (MHA) determination the extraction procedure was carried out using 0.1 M NaOH solution. Dissolved organic carbon (DOC) was analyzed using an ion chromatograph SKALAR. pH was measured in 1M H2O. N total was determined by Kjeldahl method. Results: Based on the obtained results, it can be stated that transformation of chemical composition is going through the genetic soil horizons. Morphology of the upper layers of soil profile which is formed under natural conditions was changed by anthropomorphic (agrogenic, urbogenic, technogenic and others) structure. Anthropogenic activities, mechanical and biochemical disturbances destroy the natural characteristics of soil formation and complicates the interpretation of soil development. Due to the intensive cultivation, the pH values of the curve equals (disappears acidification characteristic for E horizon) with natural Luvisol. Luvisols affected by agricultural activities was characterized by a decrease in the absolute amount of humic substances in separate horizons. But there was observed more sustainable, higher carbon sequestration and thicker storage of humic horizon compared with forest Luvisol. However, the average content of humic substances in the soil profile was lower. Soil organic carbon content in anthropogenic Luvisols was lower compared with the natural forest soil, but there was more evenly spread over in the wider thickness of accumulative horizon. These data suggest that the organization of geo-ecological declines and agroecological increases in Luvisols. Acknowledgement: This work was supported by the National Science Program ‘The effect of long-term, different-intensity management of resources on the soils of different genesis and on other components of the agro-ecosystems’ [grant number SIT-9/2015] funded by the Research Council of Lithuania.

Keywords: agrogenization, dissolved organic carbon, luvisol, mobile humic acids, soil organic carbon

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Authors: Anjan Hazra, Nirjhar Dasgupta, Chandan Sengupta, Sauren Das

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Tea (Camellia sinensis) has received substantial attention from the scientific world time to time, not only for its commercial importance, but also for its demand to the health-conscious people across the world for its extensive use as potential sources of antioxidant supplement. These health-benefit traits primarily rely on some regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions is being worthwhile for studying the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea the trait-specific Simple Sequence Repeats (SSRs) are yet to be identified, which can be used for marker assisted breeding technique. MicroRNAs are endogenous, noncoding, short RNAs directly involved in regulating gene expressions at the post-transcriptional level. It has been found that diversity in miRNA gene interferes the formation of its characteristic hair pin structure and the subsequent function. In the present study, the precursors of small regulatory RNAs (microRNAs) has been fished out from tea Expressed Sequence Tag (EST) database. Furthermore, the simple sequence repeat motifs within the putative miRNA precursor genes are also identified in order to experimentally validate their existence and function. It is already known that genic-SSR markers are very adept and breeder-friendly source for genetic diversity analysis. So, the potential outcome of this in-silico study would provide some novel clues in understanding the miRNA-triggered polymorphic genic expression controlling specific metabolic pathways, accountable for tea quality.

Keywords: micro RNA, simple sequence repeats, tea quality, trait specific marker

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Authors: Ragy Raafat Gaber Attaalla

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For cardiovascular illness, oral P2Y12 inhibitors including clopidogrel, prasugrel, and ticagrelor are frequently recommended. Each of these medications has advantages and disadvantages. In the absence of genotyping, it has been demonstrated that the stronger platelet aggregation inhibitors prasugrel and ticagrelor are superior than clopidogrel at preventing significant adverse cardiovascular events following an acute coronary syndrome and percutaneous coronary intervention (PCI). Both, nevertheless, come with a higher risk of bleeding unrelated to a coronary artery bypass. As a prodrug, clopidogrel needs to be bioactivated, principally by the CYP2C19 enzyme. A CYP2C19 no function allele and diminished or absent CYP2C19 enzyme activity are present in about 30% of people. The reduced exposure to the active metabolite of clopidogrel and reduced inhibition of platelet aggregation among clopidogrel-treated carriers of a CYP2C19 no function allele likely contributed to the reduced efficacy of clopidogrel in clinical trials. Clopidogrel's pharmacogenetic results are strongest when used in conjunction with PCI, but evidence for other indications is growing. One of the most typical examples of clinical pharmacogenetic application is CYP2C19 genotype-guided antiplatelet medication following PCI. Guidance is available from expert consensus groups and regulatory bodies to assist with incorporating genetic information into P2Y12 inhibitor prescribing decisions. Here, we examine the data supporting genotype-guided P2Y12 inhibitor selection's effects on clopidogrel response and outcomes and discuss tips for pharmacogenetic implementation. We also discuss procedures for using genotype data to choose P2Y12 inhibitor therapies as well as any unmet research needs. Finally, choosing a P2Y12 inhibitor medication that optimally balances the atherothrombotic and bleeding risks may be influenced by both clinical and genetic factors.

Keywords: inhibitors, cardiovascular events, coronary intervention, pharmacogenetic implementation

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Authors: Dharshika Rajalingam, Jeffery W. Peng

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Acinetobacter baumannii is a challenging threat to global health, recognized as a multidrug-resistant pathogen. -lactamase is one of the principal resistant mechanisms developed by A. baumannii to survive against -lactam antibiotics. OXA24/40 is one of the types of -lactamases, a well-documented carbapenem hydrolyzing class D -lactamases (CHDL). It was revealed that OXA24/40 showed resistivity against doripenem, one of the carbapenems, by two different mechanisms as hydrolysis and -lactonization. Furthermore, it undergoes genetic mutations to broaden the -lactamase activity to survive against antibiotic environments. One of the crucial characterizations of prokaryotes to develop adaptation is post-translational modification (PTM), mainly phosphorylation. However, the PTM of OXA24/40 is an unknown feature, and the impact of PTM on antibiotic resistivity is yet to be explored. We approached these hypotheses using NMR and MS techniques and found that the OXA24/40 could be phosphorylated in vitro. The Ser81 at the active STFK motif of OXA24/40 of catalytic pocket was identified as the site of phosphorylation using 1D 31P NMR experiment, whereas S81 is required to form an acyl-enzyme complex between enzyme and -lactam antibiotics. The activity of completely phosphorylated OXA24/40 wild type against doripenem revealed that the phosphorylation of active Ser inactivates the -lactamases activity of OXA24/40. The 1D 1H CPMG NMR-based activity assay of phosphorylated OXA24/40 against doripenem confirmed that both deactivating mechanisms are inhibited by phosphorylation. Carbamylated Lysine at the active STFK motif is one of the critical features of CHDL required for the acylation and deacylation reactions of the enzyme. The 1D 13C NMR experiment confirmed that the K84 of phosphorylated OXA24/40 is de-carbamylated. Phosphorylation of OXA24/40 affects both active S81 and carbamylated K84 of OXA24 that are required for the resistivity of -lactamase. So, phosphorylation could be one of the reasons for the genetic mutation of OXA24/40 for the development of antibiotic resistivity. Further research can lead to an understanding of the effect of phosphorylation on the clinical mutants of the OXA24-like -lactamase family on the broadening of -lactamase activity.

Keywords: OXA24/40, phosphorylation, clinical mutants, resistivity

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Authors: Simona Perga, Chiara Beltramo, Floriana Fruscione, Isabella Martini, Federica Cavallo, Federica Riccardo, Paolo Buracco, Selina Iussich, Elisabetta Razzuoli, Katia Varello, Lorella Maniscalco, Elena Bozzetta, Angelo Ferrari, Paola Modesto

Abstract:

Introduction: Human and canine melanoma have common clinical, histologic characteristics making dogs a good model for comparative oncology. The identification of specific genes and a better understanding of the genetic landscape, signaling pathways, and tumor–microenvironmental interactions involved in the cancer onset and progression is essential for the development of therapeutic strategies against this tumor in both species. In the present study, the differential expression of genes in spontaneously occurring canine melanoma and in paired normal tissue was investigated by targeted RNAseq. Material and Methods: Total RNA was extracted from 17 canine malignant melanoma (CMM) samples and from five paired normal tissues stored in RNA-later. In order to capture the greater genetic variability, gene expression analysis was carried out using two panels (Qiagen): Human Immuno-Oncology (HIO) and Mouse-Immuno-Oncology (MIO) and the miSeq platform (Illumina). These kits allow the detection of the expression profile of 990 genes involved in the immune response against tumors in humans and mice. The data were analyzed through the CLCbio Genomics Workbench (Qiagen) software using the Canis lupus familiaris genome as a reference. Data analysis were carried out both comparing the biologic group (tumoral vs. healthy tissues) and comparing neoplastic tissue vs. paired healthy tissue; a Fold Change greater than two and a p-value less than 0.05 were set as the threshold to select interesting genes. Results and Discussion: Using HIO 63, down-regulated genes were detected; 13 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Eighteen genes were up-regulated, 14 of those were also down-regulated comparing neoplastic sample vs. paired healthy tissue. Using the MIO, 35 down regulated-genes were detected; only four of these were down-regulated, also comparing neoplastic sample vs. paired healthy tissue. Twelve genes were up-regulated in both types of analysis. Considering the two kits, the greatest variation in Fold Change was in up-regulated genes. Dogs displayed a greater genetic homology with humans than mice; moreover, the results have shown that the two kits are able to detect different genes. Most of these genes have specific cellular functions or belong to some enzymatic categories; some have already been described to be correlated to human melanoma and confirm the validity of the dog as a model for the study of molecular aspects of human melanoma.

Keywords: animal model, canine melanoma, gene expression, spontaneous tumors, targeted RNAseq

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Authors: Abubakar Maitama Yusuf Hotoro, Olokpo Israel Olofu, Yusuf U. Tarauni, Mudassir A. Umar, Aliyu A, Dahiru Garba Diso, Usman H. Jamoh, M. Sale

Abstract:

The study assessed the impact of environmental pollution on groundwater potential at Tudun Murtala waste land fill using electrical resistivity, induced polarization and Physiochemical methods. The study area is located between latitude 12.023678N and longitude 8.573676 E. Geophysical data were collected at maximum length of 140m along twelve profiles using ABEM Terrameter SAS 1000. Results from the Geophysical analysis showed that the profiles were underlain by three lithological layers; the top layer consisting of Loamy and Sand soils, alluvium, granite, shale and sandstone. The second and third layers were predominantly made of weathered and fractured basements respectively. The potential groundwater water bearing zones of the study area occurred at VES2, VES4, VES5, VES6 and VES7. The thicknesses of the sounding points were found to be 20.8m at VES2; 25.2m at VES4; 13.2m at VES5; 50.8m at VES6 and 13.3m at VES7. The corresponding depths for the sounding points were 20.8m at VES2; 27.9m at VES4; 26.7m at VES5; 51.6m at VES6 and 24.9m at VES7 respectively. The Physiochemical study of selected groundwater samples assessed parameters such as the Electrical Conductivity, EC (288dS/m to 1365dS/m), TDS (170.8mg/L to 820mg/L) Pb (0.546mg/l to 0.629mg/l), Cu (-0.001mg/l to 0.004mg/l), and Cd (0.031mg/l to 0.092mg/l). The physiochemical results showed that the groundwater around the dumpsite may have been contaminated, especially in Dumpsite Hole 1 and Hole 2 at VES4 and VES6 respectively. There are indications for suspected leachate mitigation around the two VES points. Even though, the pH values of 6.4 and 6.2 at the two sounding points were considered to be within the permissible pH range (6.5 to 6.8). The values of other elements present in the groundwater for the samples at other VES points were found to be above permissible WHO and Nigerian Standards for Drinking Water.

Keywords: resistivity induced polarization, chargeability, landfill, leachate, contamination

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Authors: Abdulwahhab Khedr, Tamer Shehata, Hanaa El-Ghamry

Abstract:

Venlafaxine HCl is a novel antidepressant drug used in the treatment of major depressive disorder, generalized anxiety disorder, social anxiety disorder and panic disorder. Conventional therapeutic regimens with venlafaxine HCl immediate-release dosage forms require frequent dosing due to short elimination half-life of the drug and reduced bioavailability. Hence, this study was carried out to develop sustained-release dosage forms of venlafaxine HCl to reduce its dosing frequency, to improve patient compliance and to reduce side effects of the drug. The polymers used were hydroxypropylmethyl cellulose, xanthan gum, sodium alginate, sodium carboxymethyl cellulose, Carbopol 940 and ethyl cellulose. The physical properties of the prepared tablets including tablet thickness, diameter, weight uniformity, content uniformity, hardness and friability were evaluated. Also, the in-vitro release of venlafaxine HCl from different matrix tablets was studied. Based on physical characters and in-vitro release profiles, certain formulae showing promising sustained-release profiles were subjected to film coating with 15% w/v EC in dichloromethane/ethanol mixture (1:1 ratio) using 1% w/v HPMC as pore former and 30% w/w dibutyl phthalate as plasticizer. The optimized formulations were investigated for drug-excipient compatibility using FTIR and DSC studies. Physical evaluation of the prepared tablets fulfilled the pharmacopoeial requirements for tablet friability test, where the weight loss of the prepared formulae did not exceed 1% of the weight of the tested tablets. Moderate release was obtained from tablets containing HPMC. FTIR and DSC studies for such formulae revealed the absence of any type of chemical interaction between venlafaxine HCl and the used polymers or excipients. Forced swimming test in rats was used to evaluate the antidepressant activity of the selected matrix tablets of venlafaxine HCl. Results showed that formulations significantly decreased the duration of animals’ immobility during the 24 hr-period of the test compared to non-treated group.

Keywords: antidepressant, sustained-release, matrix tablet, venlafaxine hydrochloride

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Authors: C. V. Nnamani, O. L. Adedeji

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The contemporary global economic meltdown has devastating effect on the Nigerian’s economy and its frantic search for alternative source of national revenue aside from oil and gas has become imperative for economic emancipation for Nigerians. Apicultural entrepreneurship could provide a source of livelihood if the basic knowledge of those plant genetic resources needed by bees is made available. A palynological evaluation of those palynotaxa which honey bees forage for pollen and nectar was carried out after standard acetolysis method. Results showed that the honey samples were highly diversified and rich in honey plants. A total of 9544.3 honey pollen, consisting of 39 honey plants belonging to 21 plant families and distributed within 38 genera were identified excluding 238 unidentified pollen grains. Data from the analysis equally revealed that Elaeis guineensis Jacq, Anacardium occidentale L, Diospyros mespiliformis Hochist xe ADC, Alchornea cordifolia Muell, Arg, Daniella oliveri (Rolfe) Hutch & Dalz, Irvingia wombolu Okafor ex Baill, Treculia africana Decne, Nauclea latifolia Smith and Crossopteryx febrifuga Afzil ex Benth were the predominant honey plants. It provided a guide to the optimal utilization of floral resources by honeybees in these regions, showing the opportunity and amazing potentials for apiculture entrepreneurship of these palytaxa. Most of these plants are rare, threatened and endangered. It calls for urgent conservation techniques and step by all players. Critical awareness creation to ensure farmers knowledge of these palynotaxa to ensure proper understanding and attendance boost from them as economic empowerment is needed.

Keywords: palynotaxa, acetolysis, enterprise, livelihood, Nigeria

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Authors: Nanine Fouche

Abstract:

The Cape Flats is a low-lying sand-covered expanse of approximately 460 square kilometres, situated to the southeast of the central business district of Cape Town in the Western Cape of South Africa. The aeolian sands masking this area are often loose and compressible in the upper 1m to 1.5m of the surface, and there is a general exceedance of the maximum allowable settlement in these sands. The settlement of shallow foundations on Cape Flats sands is commonly predicted using the results of in-situ tests such as the SPT or DPSH due to the difficulty of retrieving undisturbed samples for laboratory testing. Varying degrees of accuracy and reliability are associated with these methods. More recently, shear wave velocity (Vs) profiles obtained from seismic testing, such as continuous surface wave tests (CSW), are being used for settlement prediction. Such predictions have the advantage of considering non-linear stress-strain behaviour of soil and the degradation of stiffness with increasing strain. CSW tests are rarely executed in the Cape Flats, whereas SPT’s are commonly performed. For this reason, and to facilitate better settlement predictions in Cape Flats sand, equations representing shear wave velocity (Vs) as a function of SPT blow count (N60) and vertical effective stress (v’) were generated by statistical regression of site investigation data. To reveal the most appropriate method of overburden correction, analyses were performed with a separate overburden term (Pa/σ’v) as well as using stress corrected shear wave velocity and SPT blow counts (correcting Vs. and N60 to Vs1and (N1)60respectively). Shear wave velocity profiles and SPT blow count data from three sites masked by Cape Flats sands were utilised to generate 80 Vs-SPT N data pairs for analysis. Investigated terrains included sites in the suburbs of Athlone, Muizenburg, and Atlantis, all underlain by windblown deposits comprising fine and medium sand with varying fines contents. Elastic settlement analysis was also undertaken for the Cape Flats sands, using a non-linear stepwise method based on small-strain stiffness estimates, which was obtained from the best Vs-N60 model and compared to settlement estimates using the general elastic solution with stiffness profiles determined using Stroud’s (1989) and Webb’s (1969) SPT N60-E transformation models. Stroud’s method considers strain level indirectly whereasWebb’smethod does not take account of the variation in elastic modulus with strain. The expression of Vs. in terms of N60 and Pa/σv’ derived from the Atlantis data set revealed the best fit with R2 = 0.83 and a standard error of 83.5m/s. Less accurate Vs-SPT N relations associated with the combined data set is presumably the result of inversion routines used in the analysis of the CSW results showcasing significant variation in relative density and stiffness with depth. The regression analyses revealed that the inclusion of a separate overburden term in the regression of Vs and N60, produces improved fits, as opposed to the stress corrected equations in which the R2 of the regression is notably lower. It is the correction of Vs and N60 to Vs1 and (N1)60 with empirical constants ‘n’ and ‘m’ prior to regression, that introduces bias with respect to overburden pressure. When comparing settlement prediction methods, both Stroud’s method (considering strain level indirectly) and the small strain stiffness method predict higher stiffnesses for medium dense and dense profiles than Webb’s method, which takes no account of strain level in the determination of soil stiffness. Webb’s method appears to be suitable for loose sands only. The Versak software appears to underestimate differences in settlement between square and strip footings of similar width. In conclusion, settlement analysis using small-strain stiffness data from the proposed Vs-N60 model for Cape Flats sands provides a way to take account of the non-linear stress-strain behaviour of the sands when calculating settlement.

Keywords: sands, settlement prediction, continuous surface wave test, small-strain stiffness, shear wave velocity, penetration resistance

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Authors: E. Keramaris

Abstract:

In this study, laboratory experiments in open channel flows over a sand bed were conducted. A porous bed (sand bed) with porosity of ε=0.70 and porous thickness of s΄=3 cm was tested. Vertical distributions of velocity were evaluated by using a two-dimensional (2D) Particle Image Velocimetry (PIV). Velocity profiles are measured above the impermeable bed and above the sand bed for the same different total water heights (h= 6, 8, 10 and 12 cm) and for the same slope S=1.5. Measurements of mean velocity indicate the effects of the bed material used (sand bed) on the flow characteristics (Velocity distribution and Reynolds number) in comparison with those above the impermeable bed.

Keywords: particle image velocimetry, sand bed, velocity distribution, Reynolds number

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Authors: Sekena H. Abd El-Aziem, Heba A. M. Abd El-Kader, Sally S. Alam, Othman E. Othman

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Growth hormone (GH) is an anabolic hormone synthesized and secreted by the somatotroph cells of the anterior lobe of the pituitary gland in a circadian and pulsatile manner, the pattern of which plays an important role in postnatal longitudinal growth and development, tissue growth, lactation, reproduction as well as protein, lipid and carbohydrate metabolism. The aim of this study was to detect the genetic polymorphism of GH gene in five camel breeds reared in Egypt; Sudany, Somali, Mowaled, Maghrabi and Falahy, using PCR-RFLP technique. Also this work aimed to identify the single nucleotide polymorphism between different genotypes detected in these camel breeds. The amplified fragment of camel GH at 613-bp was digested with the restriction enzyme MspI and the result revealed the presence of three different genotypes; CC, CT and TT in tested breeds and significant differences were recorded in the genotype frequencies between these camel breeds. The result showed that the Maghrabi breed that is classified as a dual purpose camels had higher frequency for allele C (0.75) than those in the other tested four breeds. The sequence analysis declared the presence of a SNP (C→T) at position 264 in the amplified fragment which is responsible for the destruction of the restriction site C^CGG and consequently the appearance of two different alleles C and T. The nucleotide sequences of camel GH alleles T and C were submitted to nucleotide sequences database NCBI/Bankit/GenBank and have accession numbers: KP143517 and KP143518, respectively. It is concluded that only one SNP C→T was detected in GH gene among the five tested camel breeds reared in Egypt and this nucleotide substitution can be used as a marker for the genetic biodiversity between camel breeds reared in Egypt. Also, due to the possible association between allele C and higher growth rate, we can used it in MAS for camels and enter the camels possess this allele in breeding program as a way for enhancement of growth trait in camel breeds reared in Egypt.

Keywords: camel breeds in Egypt, GH, PCR-RFLP, SNPs

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Authors: Rihab Gamaoun, Cynthia El Hage, Laura Ruiz, Erin Prosk, Antonio Vigano

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Introduction: Santé Cannabis (SC), a Canadian medical cannabis-specialized group of clinics based in Montreal and in the province of Québec, has served more than 5000 patients seeking cannabis-based treatment prescription for medical indications over the past five years. Within a research frame, data on the use of medical cannabis products from all the above patients were prospectively collected, leading to a large real-world database on the use of medical cannabis. The aim of this study was to gather information on the profiles of both patients and prescribed medical cannabis products at SC clinics and to assess the safety of medical cannabis among Canadian patients. Methods: Using a retrospective analysis of the database, records of 2585 patients who were prescribed medical cannabis products for therapeutic purposes between 01-November 2017 and 04-September 2019 were included. Patients’ demographics, primary diagnosis, route of administration, and chemovars recorded at the initial visits were investigated. Results: At baseline: 9% of SC patients were female, with a mean age of 57 (SD= 15.8, range= [18-96]); Cannabis products were prescribed mainly for patients with a diagnosis of chronic pain (65.9% of patients), cancer (9.4%), neurological disorders (6.5%), mood disorders (5.8 %) and inflammatory diseases (4.1%). Route of administration and chemovars of prescribed cannabis products were the following: 96% of patients received cannabis oil (51% CBD rich, 42.5% CBD:THC); 32.1% dried cannabis (21.3% CBD:THC, 7.4% THC rich, 3.4 CBD rich), and 2.1% oral spray cannabis (1.1% CBD:THC, 0.8% CBD rich, 0.2% THC rich). Most patients were prescribed simultaneously, a combination of products with different administration routes and chemovars. Safety analysis is undergoing. Conclusion: Our results provided initial information on the profile of medical cannabis products prescribed in a Canadian population and the experienced adverse events over the past three years. The Santé Cannabis database represents a unique opportunity for comparing clinical practices in prescribing and titrating cannabis-based medications across different centers. Ultimately real-world data, including information about safety and effectiveness, will help to create standardized and validated guidelines for choosing dose, route of administration, and chemovars types for the cannabis-based medication in different diseases and indications.

Keywords: medical cannabis, real-world data, safety, pharmacovigilance

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