Search results for: genome scale metabolic reconstruction

Authors: Luna Sequier, Florian Forelli, Maude Traulle, Amaury Vandebrouck, Pascal Duffiet, Louis Ratte, Jean Mazeas

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The study's objective is to compare the muscular activity of the flexor knee muscle in patients who underwent an anterior cruciate ligament reconstruction with hamstring autograft and the individuals who have not undergone surgery. Methods: The participants were divided into two groups: a healthy group and an experimental group who had undergone an anterior cruciate ligament reconstruction with a hamstring graft. All participants had to perform a knee flexion strength test on an isokinetic dynamometer. The medial Gastrocnemius, lateral Gastrocnemius, Biceps femoris, and medial Hamstring muscle activity were measured during this test. Each group’s mean muscle activity was tested with statistical analysis, and a muscle activity ratio of gastrocnemius and hamstring muscles was calculated Results: The results showed a significant difference in activity of the medial gastrocnemius (p = 0,004901), the biceps femoris (p = 5,394.10-6), and the semitendinosus muscles (p = 1,822.10-6), with a higher Biceps femoris and Semitendinosus activity for the experimental group. It is however noticeable that inter-subject differences were important. Conclusion: This study has shown a difference in the gastrocnemius and hamstring muscle activity between patients who underwent an anterior cruciate ligament reconstruction surgery and healthy participants. With further results, this could show a modification of muscle activity patterns after surgery which could lead to compensatory behaviors at a return to sport and eventually explain a higher injury risk for our patients.

Keywords: anterior cruciate ligament, electromyography, muscle activity, physiotherapy

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Authors: Sudikshya Bhandari, Jonathan K. London

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Barpak in northern Nepal represents a unique identity expressed through the local rituals, values, lifeways and the styles of vernacular architecture. The traditional residential buildings and construction practices adopted by the dominant ethnic groups: Ghales and Gurungs, reflect environmental, social, cultural and economic concerns. However, most of these buildings did not survive the Gorkha earthquake in 2015 that made many residents skeptical about their strength to resist future disasters. This led Barpak residents to prefer modern housing designs primarily for the strength but additionally for convenience and access to earthquake relief funds. Post-earthquake reconstruction has transformed the cohesive community, developed over hundreds of years into a haphazard settlement with the imposition of externally-driven building models. Housing guidelines provided for the community reconstruction and earthquake resilience have been used as a singular template, similar to other communities on different geographical locations. The design and construction of these buildings do not take into account the local, historical, environmental, social, cultural and economic context of Barpak. In addition to the physical transformation of houses and the settlement, the consequences continue to develop challenges to sustainability. This paper identifies the major challenges for environmental sustainability with the construction of new houses in post-earthquake Barpak. Mixed methods such as interviews, focus groups, site observation, and documentation, and analysis of housing and neighborhood design have been used for data collection. The discernible changing situation of this settlement due to the new housing has included reduced climatic adaptation and thermal comfort, increased consumption of agricultural land and water, minimized use of local building materials, and an increase in energy demand. The research has identified that reconstruction housing practices happening in Barpak, while responding to crucial needs for disaster recovery and resilience, are also leading this community towards an unsustainable future. This study has also integrated environmental, social, cultural and economic parameters into an assessment framework that could be used to develop place-based design guidelines in the context of other post-earthquake reconstruction efforts. This framework seeks to minimize the unintended repercussions of unsustainable reconstruction interventions, support the vitality of vernacular architecture and traditional lifeways and respond to context-based needs in coordination with residents.

Keywords: earthquake, environment, reconstruction, sustainability

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Authors: J. M. Lee, W. R. Noh, C. Y. Kim, M. G. Lee

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Delamination of oxide scale has been often discovered at the interface between Fe carbon steel and oxide scale. Among several mechanisms of this delamination behavior, the normal tensile stress to the substrate-scale interface has been described as one of the main factors. The stress distribution at the interface is also known to be affected by thermal expansion mismatch between substrate and oxide scale, creep behavior during cooling and the geometry of the interface. In this study, stress states near the interface in a Fe carbon steel with oxide scale have been investigated using FE simulations. The thermal and mechanical properties of oxide scales are indicated in literature and Fe carbon steel is measured using tensile testing machine. In particular, the normal and shear stress components developed at the interface during bending are investigated. Preliminary numerical sensitivity analyses are provided to explain the effects of the interface geometry and oxide thickness on the delamination behavior.

Keywords: oxide scale, delamination, Fe analysis, roughness, thickness, stress state

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Authors: P. Castillo Muñoz, A. Lara Ramírez

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Absent Theaters is a project that virtually reconstructs three theaters that existed in the twentieth century, demolished in the city of Medellin, Colombia: Circo España, Bolívar, and Junín. Virtual reconstruction is used as an excuse to talk with those who lived in their childhood and youth cultural spaces that formed a whole generation. Around 100 people who witnessed these theaters were interviewed. The means used to perform the oral history work was the virtual reconstruction of the interior of the theaters that were presented to the interviewees through the Virtual Reality glasses. The voices of people between 60 and 103 years old were used to generate a transmission of knowledge to the new generations about the importance of theaters as essential places for the city, as spaces generating social relations and knowledge of other cultures. Oral stories about events, the historical and social context of the city, were mixed with archive images and animations of the architectural transformations of these places. Oral stories about events, the historical and social context of the city, were mixed with archive images and animations of the architectural transformations of these places, with the purpose of compiling a collective discourse around cultural activities, heritage, and memory of Medellin.

Keywords: culture, heritage, oral history, theaters, virtual reality

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Authors: N. Othman, J. Ujang, M. N. Ismail, R. Noordin, B. H. Lim

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Amoebiasis is caused by the Entamoeba histolytica and still endemic in many parts of the tropical region, worldwide. Currently, there is no available vaccine against amoebiasis. Hence, there is an urgent need to develop a vaccine. The excretory secretory antigen (ESA) of E. histolytica is a suitable biomarker for the vaccine candidate since it can modulate the host immune response. Hence, the objective of this study is to identify the proteome of the ESA towards finding suitable biomarker for the vaccine candidate. The non-gel based and gel-based proteomics analyses were performed to identify proteins. Two kinds of mass spectrometry with different ionization systems were utilized i.e. LC-MS/MS (ESI) and MALDI-TOF/TOF. Then, the functional proteins classification analysis was performed using PANTHER software. Combination of the LC -MS/MS for the non-gel based and MALDI-TOF/TOF for the gel-based approaches identified a total of 273 proteins from the ESA. Both systems identified 29 similar proteins whereby 239 and 5 more proteins were identified by LC-MS/MS and MALDI-TOF/TOF, respectively. Functional classification analysis showed the majority of proteins involved in the metabolic process (24%), primary metabolic process (19%) and protein metabolic process (10%). Thus, this study has revealed the proteome the E. histolytica ESA and the identified proteins merit further investigations as a vaccine candidate.

Keywords: E. histolytica, ESA, proteomics, biomarker

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Authors: Islam Sherif, Ahmed Ashour, Ahmed Hassan, Hatem Osman

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Anterior Cruciate Ligament (ACL) injuries are common among athletes and individuals participating in sports with sudden stops, pivots, and changes in direction. Arthroscopic surgery is the gold standard for ACL reconstruction, aiming to restore knee stability and function. Recent years have witnessed significant advancements in arthroscopic surgery techniques, graft materials, and technological innovations, revolutionizing the field of ACL reconstruction. This presentation delves into the latest advancements in arthroscopic surgery techniques for ACL reconstruction and their potential impact on patient outcomes. Traditionally, autografts from the patellar tendon, hamstring tendon, or quadriceps tendon have been commonly used for ACL reconstruction. However, recent studies have explored the use of allografts, synthetic scaffolds, and tissue-engineered grafts as viable alternatives. This abstract evaluates the benefits and potential drawbacks of each graft type, considering factors such as graft incorporation, strength, and risk of graft failure. Moreover, the application of augmented reality (AR) and virtual reality (VR) technologies in surgical planning and intraoperative navigation has gained traction. AR and VR platforms provide surgeons with detailed 3D anatomical reconstructions of the knee joint, enhancing preoperative visualization and aiding in graft tunnel placement during surgery. We discuss the integration of AR and VR in arthroscopic ACL reconstruction procedures, evaluating their accuracy, cost-effectiveness, and overall impact on surgical outcomes. Beyond graft selection and surgical navigation, patient-specific planning has gained attention in recent research. Advanced imaging techniques, such as MRI-based personalized planning, enable surgeons to tailor ACL reconstruction procedures to each patient's unique anatomy. By accounting for individual variations in the femoral and tibial insertion sites, this personalized approach aims to optimize graft placement and potentially improve postoperative knee kinematics and stability. Furthermore, rehabilitation and postoperative care play a crucial role in the success of ACL reconstruction. This abstract explores novel rehabilitation protocols, emphasizing early mobilization, neuromuscular training, and accelerated recovery strategies. Integrating technology, such as wearable sensors and mobile applications, into postoperative care can facilitate remote monitoring and timely intervention, contributing to enhanced rehabilitation outcomes. In conclusion, this presentation provides an overview of the cutting-edge advancements in arthroscopic surgery techniques for ACL reconstruction. By embracing innovative graft materials, augmented reality, patient-specific planning, and technology-driven rehabilitation, orthopedic surgeons and sports medicine specialists can achieve superior outcomes in ACL injury management. These developments hold great promise for improving the functional outcomes and long-term success rates of ACL reconstruction, benefitting athletes and patients alike.

Keywords: arthroscopic surgery, ACL, autograft, allograft, graft materials, ACL reconstruction, synthetic scaffolds, tissue-engineered graft, virtual reality, augmented reality, surgical planning, intra-operative navigation

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Miroslava Cuperlovic-Culf, Lipu Wang, Ketty Boyle, Nadine Makley, Ian Burton, Anissa Belkaid, Mohamed Touaibia, Marc E. Surrette

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Metabolic changes are one of the major factors in the development of a variety of diseases in various species. Metabolism of agricultural plants is altered the following infection with pathogens sometimes contributing to resistance. At the same time, pathogens use metabolites for infection and progression. In humans, metabolism is a hallmark of cancer development for example. Quantified metabolomics data combined with other omics or clinical data and analyzed using various unsupervised and supervised methods can lead to better diagnosis and prognosis. It can also provide information about resistance as well as contribute knowledge of compounds significant for disease progression or prevention. In this work, different methods for metabolomics quantification and analysis from Nuclear Magnetic Resonance (NMR) measurements that are used for investigation of disease development in wheat and human cells will be presented. One-dimensional 1H NMR spectra are used extensively for metabolic profiling due to their high reliability, wide range of applicability, speed, trivial sample preparation and low cost. This presentation will describe a new method for metabolite quantification from NMR data that combines alignment of spectra of standards to sample spectra followed by multivariate linear regression optimization of spectra of assigned metabolites to samples’ spectra. Several different alignment methods were tested and multivariate linear regression result has been compared with other quantification methods. Quantified metabolomics data can be analyzed in the variety of ways and we will present different clustering methods used for phenotype determination, network analysis providing knowledge about the relationships between metabolites through metabolic network as well as biomarker selection providing novel markers. These analysis methods have been utilized for the investigation of fusarium head blight resistance in wheat cultivars as well as analysis of the effect of estrogen receptor and carbonic anhydrase activation and inhibition on breast cancer cell metabolism. Metabolic changes in spikelet’s of wheat cultivars FL62R1, Stettler, MuchMore and Sumai3 following fusarium graminearum infection were explored. Extensive 1D 1H and 2D NMR measurements provided information for detailed metabolite assignment and quantification leading to possible metabolic markers discriminating resistance level in wheat subtypes. Quantification data is compared to results obtained using other published methods. Fusarium infection induced metabolic changes in different wheat varieties are discussed in the context of metabolic network and resistance. Quantitative metabolomics has been used for the investigation of the effect of targeted enzyme inhibition in cancer. In this work, the effect of 17 β -estradiol and ferulic acid on metabolism of ER+ breast cancer cells has been compared to their effect on ER- control cells. The effect of the inhibitors of carbonic anhydrase on the observed metabolic changes resulting from ER activation has also been determined. Metabolic profiles were studied using 1D and 2D metabolomic NMR experiments, combined with the identification and quantification of metabolites, and the annotation of the results is provided in the context of biochemical pathways.

Keywords: metabolic biomarkers, metabolic network, metabolomics, multivariate linear regression, NMR quantification, quantified metabolomics, spectral alignment

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Authors: Somia Bouzid, Messaoud Ramdani

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The success of any diagnosis strategy critically depends on the sensors measuring process variables. This paper presents a detection and diagnosis sensor faults method based on a Bottleneck Neural Network (BNN). The BNN approach is used as a statistical process control tool for drinking water distribution (DWD) systems to detect and isolate the sensor faults. Variable reconstruction approach is very useful for sensor fault isolation, this method is validated in simulation on a nonlinear system: actual drinking water distribution system. Several results are presented.

Keywords: fault detection, localization, PCA, NLPCA, auto-associative neural network

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Authors: Muhammad Shahzad Iqbal, Zobia Sarwar, Salah-ud-Din

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Tomato spotted wilt virus (TSWV) belongs to the genus Tospoviruses (family Bunyaviridae). It is one of the most devastating pathogens of tomato (Solanum Lycopersicum) and heavily damages the crop yield each year around the globe. In this study, we retrieved 329 mature miRNA sequences from two microRNA databases (miRBase and miRSoldb) and checked the putative target sites in the downloaded-genome sequence of TSWV. A consensus of three miRNA target prediction tools (RNA22, miRanda and psRNATarget) was used to screen the false-positive microRNAs targeting sites in the TSWV genome. These tools calculated different target sites by calculating minimum free energy (mfe), site-complementarity, minimum folding energy and other microRNA-mRNA binding factors. R language was used to plot the predicted target-site data. All the genes having possible target sites for different miRNAs were screened by building a consensus table. Out of these 329 mature miRNAs predicted by three algorithms, only eight miRNAs met all the criteria/threshold specifications. MC-Fold and MC-Sym were used to predict three-dimensional structures of miRNAs and further analyzed in USCF chimera to visualize the structural and conformational changes before and after microRNA-mRNA interactions. The results of the current study show that the predicted eight miRNAs could further be evaluated by in vitro experiments to develop TSWV-resistant transgenic tomato plants in the future.

Keywords: tomato spotted wild virus (TSWV), Solanum lycopersicum, plant virus, miRNAs, microRNA target prediction, mRNA

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Authors: Narin Salehiyan, Ramin Ghasemi Shayan

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In order to investigate coronavirus RNA replication, transcription, recombination, protein processing and transport, virion assembly, the identification of coronavirus-specific cell receptors, and polymerase processing, the manipulation of coronavirus clones and complementary DNAs (cDNAs) of defective-interfering (DI) RNAs is the subject of this chapter. The idea of the Covid genome is nonsegmented, single-abandoned, and positive-sense RNA. When compared to other RNA viruses, its size is significantly greater, ranging from 27 to 32 kb. The quality encoding the enormous surface glycoprotein depends on 4.4 kb, encoding a forcing trimeric, profoundly glycosylated protein. This takes off exactly 20 nm over the virion envelope, giving the infection the appearance-with a little creative mind of a crown or coronet. Covid research has added to the comprehension of numerous parts of atomic science as a general rule, like the component of RNA union, translational control, and protein transport and handling. It stays a fortune equipped for creating startling experiences.

Keywords: covid-19, corona, virus, genome, genetic

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Authors: Muralisankar Thirunavukkarasu, Saravana Bhavan Periyakali, Santhanam Perumal

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The present study was performed to assess the effects of dietary copper (Cu) on growth, biochemical constituents, digestive enzyme activities, enzymatic antioxidant and metabolic enzymes of the freshwater prawn, Macrobrachium rosenbergii post larvae (PL). The Cu was supplemented at 0, 10, 20, 40, 60 and 80 mg kg-1 with the basal diets. Cu supplemented diets were fed to M. rosenbergii PL for a period of 90 days. At the end of the feeding experiment, 40 mg kg-1 Cu supplemented feeds fed PL showed significant (P < 0.05) improvement in survival, growth, digestive enzyme activities and concentrations of biochemical constituents. However, PL fed with 60 to 80 mg Cu kg-1 showed negative performance. Activities of enzymatic antioxidants, metabolic enzymes and lipid peroxidation in the muscle and hepatopancreas showed insignificant alterations (P > 0.05) up to 40 mg kg-1 Cu supplemented feeds fed PL. Whereas, 60 and 80 mg of Cu kg-1 supplemented feeds fed PL showed significant alterations on these antioxidants and metabolic enzymes levels. It indicates that beyond 40 mg Cu kg-1 diets were produced some toxic to M. rosenbergii PL. Therefore, the present study suggests that 40 mg Cu kg-1 can be supplemented in the diets of M. rosenbergii PL for regulating better survival and growth.

Keywords: antioxidants, biochemical constituents, copper, growth, Macrobrachium rosenbergii

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Authors: Pule P. Mpopetsi, Warren M. Potts, Nicola James, Amber Childs

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Increased CO₂ production and the consequent ocean acidification (OA) have been identified as one of the greatest threats to both calcifying and non-calcifying marine organisms. Traditionally, marine fishes, as non-calcifying organisms, were considered to have a higher tolerance to near-future OA conditions owing to their well-developed ion regulatory mechanisms. However, recent studies provide evidence to suggest that they may not be as resilient to near-future OA conditions as previously thought. In addition, earlier life stages of marine fishes are thought to be less tolerant than juveniles and adults of the same species as they lack well-developed ion regulatory mechanisms for maintaining homeostasis. This study focused on the effects of near-future OA on larval Argyrosomus japonicus, an estuarine-dependent marine fish species, in order to identify the tipping point of tolerance for the larvae of this species. Larval A. japonicus in the present study were reared from the egg up to 22 days after hatching (DAH) under three treatments. The three treatments, (pCO₂ 353 µatm; pH 8.03), (pCO₂ 451 µatm; pH 7.93) and (pCO₂ 602 µatm; pH 7.83) corresponded to levels predicted to occur in year 2050, 2068 and 2090 respectively under the Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (IPCC RCP) 8.5 model. Size-at-hatch, growth, development, and metabolic responses (standard and active metabolic rates and metabolic scope) were assessed and compared between the three treatments throughout the rearing period. Five earlier larval life stages (hatchling – flexion/post-flexion) were identified by the end of the experiment. There were no significant differences in size-at-hatch (p > 0.05), development or the active metabolic (p > 0.05) or metabolic scope (p > 0.05) of fish in the three treatments throughout the study. However, the standard metabolic rate was significantly higher in the year 2068 treatment but only at the flexion/post-flexion stage which could be attributed to differences in developmental rates (including the development of the gills) between the 2068 and the other two treatments. Overall, the metabolic scope was narrowest in the 2090 treatment but varied according to life stage. Although not significantly different, metabolic scope in the 2090 treatment was noticeably lower at the flexion stage compared to the other two treatments, and the development appeared slower, suggesting that this could be the stage most prone to OA. The study concluded that, in isolation, OA levels predicted to occur between 2050 and 2090 will not negatively affect size-at-hatch, growth, development, and metabolic responses of larval A. japonicus up to 22 DAH (flexion/post-flexion stage). The present study also identified the tipping point of tolerance (where negative impacts will begin) in larvae of the species to be between the years 2090 and 2100.

Keywords: climate change, ecology, marine, ocean acidification

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Authors: Riin Seema

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Guidance and counseling as a whole-school responsibility is a global trend. Counseling is a specific competence, that consist of cognitive, emotional, attitudinal, and behavioral components. To authors best knowledge, there are no self-assessment scales for teachers in the whole world to measure teachers’ counseling competency. In 2016 an Estonian scale on teachers counseling competence was developed during an Interdisciplinary Project at Tallinn University. The team consisted of 10 interdisciplinary students (psychology, nursery school, special and adult education) and their supervisor. In 2017 another international Interdisciplinary Project was carried out for adapting the scale in English for international students. Firstly, the Estonian scale was translated by 2 professional translators, and then a group of international Erasmus students (again from psychology, nursery school, special and adult education) selected the most suitable translation for the scale. The developed ‘Teacher’s Counselling Competence Self-Efficacy Scale’ measures teacher’s self-efficacy beliefs in their own competence to perform different counseling tasks (creating a counseling relationship, using different reflection techniques, etc.). The scale consists of 47 questions in a 5-point numeric scale. The scale is created based on counseling theory and scale development and validation theory. The scale has been used as a teaching and learning material for counseling courses by 174 Estonian and 10 international student teachers. After filling out the scale, the students also reflected on the scale and their own counseling competencies. The study showed that the scale is unidimensional and has an excellent Cronbach alpha coefficient. Student’s qualitative feedback on the scale has been very positive, as the scale supports their self-reflection. In conclusion, the developed ‘Teacher’s Counselling Competence Self-Efficacy Scale’ is a useful tool for supporting student teachers’ learning.

Keywords: competency, counseling, self-efficacy, teacher students

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Authors: Prasanjit Das, M. M. K. Khan, M. G. Rasul, Jie Wu, I. Youn

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Mineral scale formation is undoubtedly a more serious problem in the mineral industry than other process industries. To better understand scale growth and suppression, an experimental model is proposed in this study for supersaturated crystallised solutions commonly found in mineral process plants. In this experiment, surface crystallisation of potassium nitrate (KNO3) on the wall of the agitation tank and agitation effects on the scale growth and suppression are studied. The new quantitative scale suppression model predicts that at lower agitation speed, the scale growth rate is enhanced and at higher agitation speed, the scale suppression rate increases due to the increased flow erosion effect. A lab-scale agitation tank with and without baffles were used as a benchmark in this study. The fluid dynamic effects on scale growth and suppression in the agitation tank with three different size impellers (diameter 86, 114, 160 mm and model A310 with flow number 0.56) at various ranges of rotational speed (up to 700 rpm) and solution with different concentration (4.5, 4.75 and 5.25 mol/dm3) were investigated. For more elucidation, the effects of the different size of the impeller on wall surface scale growth and suppression rate as well as bottom settled scale accumulation rate are also discussed. Emphasis was placed on applications in the mineral industry, although results are also relevant to other industrial applications.

Keywords: agitation tank, crystallisation, impeller speed, scale

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Authors: A. Magno-França, A. M. Magalhães-Neto, F. Bachini, E. Cataldi, A. Bassini, L. C. Cameron

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Sprint canoeing (SC) is part of the Olympic Games since 1936. Athletes compete in solo or double races of 200m and 1000m (40 sec and 240 sec, respectively). Due to its high intensity and duration, SC is extremely useful to study the blood kinetics of some metabolites in high energetic demand. Sportomics is a field of study combining “-omics” sciences with classical biochemical analyses in order to understand sports induced systemic changes. Here, we compare Sportomics findings during SC training sessions to describe metabolic responses of five top-level canoeists. Five Olympic world-class male athletes were evaluated during two days of training.

Keywords: biochemistry of exercise, metabolomics, injury markers, sportomics

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Authors: Ahmed A. M. Shoaib, Heba A. Esaily, Mahmoud M. Emara, Eman A. E. Badr, Amany S. Khalifa, Mayada M. M., Abdel-Raizk

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Background: DM is associated with metabolic bone diseases, osteoporosis, low-impact fractures and falls in geriatrics. Fetuin-A, which is a serum protein produced by the liver and promotes bone mineralization, is an independent risk factor for type 2 diabetes. Aim: Evaluation of fetuin-A level and bone mineral density in postmenopausal Egyptian female patients with type 2 diabetes mellitus and their correlation with each other & with other metabolic parameters. Patients and methods: Seventy postmenopausal female patients with type II diabetes and thirty postmenopausal female as control were included in this study. Measurement of Fetuin-A together with metabolic parameters and DXA in wrist, hip and spine, ALP, CBC, FBS, PP2H and HBA1c was done in all participants. Results: - Fetuin-A level was found to be highly significant (p< 0.001) between diabetic and nondiabetic groups and negatively correlated with BMD in spine. No difference in BMD was found between patients and control groups while significant negative correlation was found between FBS and hip BMD (<0.05) and between 2hpp and HBA1c with spine BMD in the diabetic group (<0.05). Osteoporosis represented 12.9% in spine area and 7.2% in hip and wrist areas in diabetic patients, while osteopenia were found in 58.5%, 57.1%, and 37.1% in diabetic patients in spine, wrist, and hip respectively. Conclusion: - type II diabetes cannot be considered as a risk factor for osteoporosis; while glycemic parameters (FBS, 2hpp & HBA1c) and serum Fetuin-A levels were correlated with BMD in diabetics. Good glycemic control can be protective against osteoporosis in diabetic elderly.

Keywords: fetuin-A, BMD, postmenopausal, DM type II

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Authors: V. V. Povoroznyuk, Lar. P. Martynyuk, N. I. Dzerovych, Lil. P. Martyntyuk

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Objective: Menopause-related changes in female body are associated with the greater risk of metabolic syndrome (MS), which includes obesity, dyslipidemia, impaired glucose tolerance, hypertension. The aim of our study was to reveal peculiarities of fat and lean mass distribution between postmenopausal women with abdominal obesity and with MS. Materials and Methods: The sample consisted of 43 postmenopausal 60 – 69 years old women (age: mean = 64,8; S.D. = 0,4); duration of menopause: mean = 14,5; S.D.= 0,9). The diagnosis of MS was considered according to IDF (2005 yr) criteria. Lean and fat mass distrubution were measured by dual-energy X-ray absortiometry, and were compared for the cohorts with and without MS. Data were analyzed using Statistical Package 6.0 (Statsoft). Results: Findings revealed that 24 (55,8 %) of postmenopausal women had MS. In patients with and without MS compared, fat mass was higher in the former group (41248,25±2263,89 and 29817,68±2397,78 respectively; F=11,9; p=0,001) and at different body regions also: gynoid fat (6563,72±348,19 and 5115,21±392,43 respectively; F=7,6; p=0,008), android fat (3815,45±200,8128 and 2798,15±282,79 respectively; F=9,06; p=0,004. Lean mass comparing didn’t show significant differences in female with and without MS (42548,0±1239,18 and 40667,53±1223,78 respectively; F=1,1; p=0,29) and at different body regions also. Conclusion: These findings suggest that in postmenopausal women with MS there is prevalence of fat mass without increasing of lean mass quantity in compare to female with abdominal obesity without MS.

Keywords: lean mass, fat mass, овesity, metabolic syndrome, women, postmenopausal period

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Authors: Charles Lee

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The Principal Orthogonal Decomposition (POD) technique has been used as a model reduction tool for many applications in engineering and science. In principle, one begins with an ensemble of data, called snapshots, collected from an experiment or laboratory results. The beauty of the POD technique is that when applied, the entire data set can be represented by the smallest number of orthogonal basis elements. It is the such capability that allows us to reduce the complexity and dimensions of many physical applications. Mathematical formulations and numerical schemes for the POD method will be discussed along with applications in NASA’s Deep Space Large Antenna Arrays, Satellite Image Reconstruction, Cancer Detection with DNA Microarray Data, Maximizing Stock Return, and Medical Imaging.

Keywords: reduced-order methods, principal component analysis, cancer detection, image reconstruction, stock portfolios

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Authors: Ting-Chia Lien, Tzu-Yin Yen, Szu-Fan Chen, Tai-chun Kuo, Hung-Tse Lin, Yi-Chen Chung, Hock-Sen Gwee

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The purpose of this study was to explore the result of the survey by developing “Self-Concept Scale for Elders”, which could provide community counseling and guidance institution for practical application. The sample of this study consisted of 332 elders in Taiwan (male: 33.4%; female: 66.6%). The mean age of participants was 65-98 years. The measurements applied in this study is “Self-Concept Scale for Elders”. After item and factor analyses, the preliminary version of the Self-Concept Scale for Elders was revised to the final version. The results were summarized as follows: 1) There were 10 items in Self-Concept Scale for Elders. 2) The variance explained for the scale accounted for 77.15%, with corrected item-total correlations Cronbach’s alpha=0.87. 3) The content validity, criterion validity and construct validity have been found to be satisfactory. Based on the findings, the implication and suggestions are offered for reference regarding counselor education and future research.

Keywords: self-concept, elder, development scale, applied psychology

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

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Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

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Authors: Patricia Agboro

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The definition of a concept is quite important in any philosophical discourse as it serves as a guide in the analysis of that concept. In the sciences, arriving at a consensus regarding concepts is quite easily achievable due to the nature of the discipline. Problem arises when one delves into the realm of the humanities. Discourses in the humanities are largely perspectival because the question of values come into play. Defining the concept of Art is no different as it has yielded unresolved and problematic issues arising from attempts at definition. A major problem arising from such attempt is that of exclusion of other art forms. In this paper therefore, we call for the rejection of an attempt at providing a comprehensive definition for Art since it is clear that the collection of definitions provided so far, has failed in capturing the nuances and intricacies of the infinite varieties of the art forms that there are. Rather, a more fruitful approach to philosophical discourses on Art is not to construe the theories of Art per-se but to reconstruct them as a collection of criteria for determining artistic excellence.

Keywords: art, creativity, definition, reconstruction

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Authors: Muhammad Fiaz, Muhammad Saqlain, Bernard M. Y. Cheung, S. M. Saqlan Naqvi, Ghazala Kaukab Raja

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Background: Association of C allele of rs662799 SNP of APOA5 gene with metabolic syndrome (MetS) has been reported in different populations around the world. A case control study was conducted to explore the relationship of rs662799 variants (T/C) with the MetS and the associated risk phenotypes in a population of Pakistani origin. Methods: MetS was defined according to the IDF criteria. Blood samples were collected from the Pakistan Institute of Medical Sciences, Islamabad, Pakistan for biochemical profiling and DNA extraction. Genotyping of rs662799 was performed using mass ARRAY, iPEX Gold technology. A total of 712 unrelated case and control subjects were genotyped. Data were analyzed using Plink software and SPSS 16.0. Results: The risk allele C of rs662799 showed highly significant association with MetS (OR=1.5, Ρ=0.002). Among risk phenotypes, dyslipidemia, and obesity showed strong association with SNP (OR=1.49, p=0.03; OR =1.46, p=0.01) respectively in models adjusted for age and gender. Conclusion: The rs662799C allele is a significant risk marker for MetS in the local Pakistani population studied. The effect of the SNP is more on dyslipidemia than the other components of the MetS.

Keywords: metabolic syndrome, APOA5, rs662799, dyslipidemia, obesity

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Authors: Xin Wang, Munkbayar Munkhjargal, Kumiko Miyajima, Takahiro Arakawa, Kohji Mitsubayashi

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The measurement of gaseous ethanol plays an important role of evaluation of alcohol metabolic capacity in clinical and forensic analysis. A 2-dimensional visualization system for gaseous ethanol was constructed and tested in visualization of breath and transdermal alcohol. We demonstrated breath ethanol measurement using developed high-sensitive visualization system. The concentration of breath ethanol calculated with the imaging signal was significantly different between the volunteer subjects of ALDH2 (+) and (-).

Keywords: breath ethanol, ethnaol imaging, biochemical luminescence, alcohol metabolism

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Authors: Kgaugelo Lekota, Ayesha Hassim, Henriette Van Heerden

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Bacillus anthracis is the causative agent of anthrax that is composed of three genetic groups, namely A, B, and C. Clade-A is distributed world-wide, while sub-clades B has been identified in Kruger National Park (KNP), South Africa. KNP is one of the endemic anthrax regions in South Africa with distinctive genetic diversity. Genomic surveillance of KNP B. anthracis strains was employed on the historical culture collection isolates (n=67) dated from the 1990’s to 2015 using a whole genome sequencing approach. Whole genome single nucleotide polymorphism (SNPs) and pan-genomics analysis were used to define the B. anthracis genetic population structure. This study showed that KNP has heterologous B. anthracis strains grouping in the A-clade with more prominent ABr.005/006 (Ancient A) SNP lineage. The 2012 and 2015 anthrax isolates are dispersed amongst minor sub-clades that prevail in non-stabilized genetic evolution strains. This was augmented with non-parsimony informative SNPs of the B. anthracis strains across minor sub-clades of the Ancient A clade. Pan-genomics of B. anthracis showed a clear distinction between A and B-clade genomes with 11 374 predicted clusters of protein coding genes. Unique accessory genes of B-clade genomes that included biosynthetic cell wall genes and multidrug resistant of Fosfomycin. South Africa consists of diverse B. anthracis strains with unique defined SNPs. The sequenced B. anthracis strains in this study will serve as a means to further trace the dissemination of B. anthracis outbreaks globally and especially in South Africa.

Keywords: bacillus anthracis, whole genome single nucleotide polymorphisms, pangenomics, kruger national park

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Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: manihot esculenta crantz, plant architecture, dartseq, snp markers, genome-wide association study

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Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu

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Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.

Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence

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Authors: R. Sulakshana, R. Lakshmi

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Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR associate (CRISPR/Cas) is an adaptive immunity system found in bacteria and archaea. It has been modified to serve as a potent gene editing tool. Moreover, it has found widespread use in the field of genome research because of its accessibility and low cost. Several bioinformatics methods have been created to aid in the construction of specific single guide RNA (sgRNA), which is highly active and crucial to CRISPR/Cas performance. Various Cas proteins, including Cas1, Cas2, Cas9, and Cas12, have been used to create genome engineering tools because of their programmable sequence specificity. Class 1 and 2 CRISPR/Cas systems, as well as the processes of all known Cas proteins (including Cas9 and Cas12), are discussed in this review paper. In addition, the various CRISPR methodologies and their tools so far discovered are discussed. Finally, the challenges and issues in the CRISPR system along with future works, are presented.

Keywords: gene editing tool, Cas proteins, CRISPR, guideRNA, programmable sequence

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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A huge revolution has emerged in genome engineering by the discovery of CRISPR (clustered regularly interspaced palindromic repeats) and CRISPR-associated system genes (Cas) in bacteria. The function of type II Streptococcus pyogenes (Sp) CRISPR/Cas9 system has been confirmed in various species. Other S. thermophilus (St) CRISPR-Cas systems, CRISPR1-Cas and CRISPR3-Cas, have been also reported for preventing phage infection. The CRISPR1-Cas system interferes by cleaving foreign dsDNA entering the cell in a length-specific and orientation-dependant manner. The S. thermophilus CRISPR3-Cas system also acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed in the CRISPR1-Cas system. It is worth mentioning, for the effective DNA cleavage activity, RNA-guided Cas9 orthologs require their own specific PAM (protospacer adjacent motif) sequences. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of target site for the three orthogonals of Cas9 protein, a well-organized procedure will be required for high-throughput and accurate mining of possible target sites in a large genomic dataset. Consequently, we created a reliable procedure to explore potential gRNA sequences for type I (Streptococcus thermophiles), II (Streptococcus pyogenes), and III (Streptococcus thermophiles) CRISPR/Cas systems. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows: i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. The output of such procedure highlights the power of comparative genome mining for different CRISPR/Cas systems. This could yield a repertoire of Cas9 variants with expanded capabilities of gRNA design, and will pave the way for further advance genome and epigenome engineering.

Keywords: CRISPR/Cas systems, gRNA mining, Streptococcus pyogenes, Streptococcus thermophiles

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