Search results for: sequence variants

Authors: Elif Tugce Aksun Tumerkan

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Although seafood is an important part of human diet and categorized highly traded food industry internationally, it is remain overlooked generally in the global food security aspect. Food product authentication is the main interest in the aim of both avoids commercial fraud and to consider the risks that might be harmful to human health safety. In recent years, with increasing consumer demand for regarding food content and it's transparency, there are some instrumental analyses emerging for determining food fraud depend on some analytical methodologies such as proteomic and metabolomics. While, fish and seafood consumed as fresh previously, within advanced technology, processed or packaged seafood consumption have increased. After processing or packaging seafood, morphological identification is impossible when some of the external features have been removed. The main fish and seafood quality-related issues are the authentications of seafood contents such as mislabelling products which may be contaminated and replacement partly or completely, by lower quality or cheaper ones. For all mentioned reasons, truthful consistent and easily applicable analytical methods are needed for assurance the correct labelling and verifying of seafood products. DNA-barcoding methods become popular robust that used in taxonomic research for endangered or cryptic species in recent years; they are used for determining food traceability also. In this review, when comparing the other proteomic and metabolic analysis, DNA-based methods are allowing a chance to identification all type of food even as raw, spiced and processed products. This privilege caused by DNA is a comparatively stable molecule than protein and other molecules. Furthermore showing variations in sequence based on different species and founding in all organisms, make DNA-based analysis more preferable. This review was performed to clarify the main advantages of using DNA-barcoding for determining seafood fraud among other techniques.

Keywords: DNA-barcoding, genetic analysis, food fraud, mislabelling, packaged seafood

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Authors: Pavlina Capkova, Josef Srovnal, Vera Becvarova, Marie Trkova, Zuzana Capkova, Andrea Stefekova, Vaclava Curtisova, Alena Santava, Sarka Vejvalkova, Katerina Adamova, Radek Vodicka

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ASDs are heterogeneous and complex developmental diseases with a significant genetic background. Recurrent CNVs are known to be a frequent cause of ASD. These CNVs can have, however, a variable expressivity which results in a spectrum of phenotypes from asymptomatic to ID/DD/ASD. ASD is associated with ID in ~75% individuals. Various platforms are used to detect pathogenic mutations in the genome of these patients. The performed study is focused on a determination of the frequency of pathogenic mutations in a group of ASD patients and a group of ID/DD patients using various strategies along with a comparison of their detection rate. The possible role of the origin of these mutations in aetiology of ASD was assessed. The study included 35 individuals with ASD and 68 individuals with ID/DD (64 males and 39 females in total), who underwent rigorous genetic, neurological and psychological examinations. Screening for pathogenic mutations involved karyotyping, screening for FMR1 mutations and for metabolic disorders, a targeted MLPA test with probe mixes Telomeres 3 and 5, Microdeletion 1 and 2, Autism 1, MRX and a chromosomal microarray analysis (CMA) (Illumina or Affymetrix). Chromosomal aberrations were revealed in 7 (1 in the ASD group) individuals by karyotyping. FMR1 mutations were discovered in 3 (1 in the ASD group) individuals. The detection rate of pathogenic mutations in ASD patients with a normal karyotype was 15.15% by MLPA and CMA. The frequencies of the pathogenic mutations were 25.0% by MLPA and 35.0% by CMA in ID/DD patients with a normal karyotype. CNVs inherited from asymptomatic parents were more abundant than de novo changes in ASD patients (11.43% vs. 5.71%) in contrast to the ID/DD group where de novo mutations prevailed over inherited ones (26.47% vs. 16.18%). ASD patients shared more frequently their mutations with their fathers than patients from ID/DD group (8.57% vs. 1.47%). Maternally inherited mutations predominated in the ID/DD group in comparison with the ASD group (14.7% vs. 2.86 %). CNVs of an unknown significance were found in 10 patients by CMA and in 3 patients by MLPA. Although the detection rate is the highest when using CMA, recurrent CNVs can be easily detected by MLPA. CMA proved to be more efficient in the ID/DD group where a larger spectrum of rare pathogenic CNVs was revealed. This study determined that maternally inherited highly penetrant mutations and de novo mutations more often resulted in ID/DD without ASD in patients. The paternally inherited mutations could be, however, a source of the greater variability in the genome of the ASD patients and contribute to the polygenic character of the inheritance of ASD. As the number of the subjects in the group is limited, a larger cohort is needed to confirm this conclusion. Inherited CNVs have a role in aetiology of ASD possibly in combination with additional genetic factors - the mutations elsewhere in the genome. The identification of these interactions constitutes a challenge for the future. Supported by MH CZ – DRO (FNOl, 00098892), IGA UP LF_2016_010, TACR TE02000058 and NPU LO1304.

Keywords: autistic spectrum disorders, copy number variant, chromosomal microarray, intellectual disability, karyotyping, MLPA, multiplex ligation-dependent probe amplification

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Authors: Debit Datta, Jeffrey J. Coleman, Scott A. Enebak, Lori G. Eckhardt

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Loblolly pine (Pinus taeda) is a leading productive timber species in the southeastern USA. Over the past three years, an emerging threat is expressed by successive needle defoliation followed by stunted growth and tree mortality in loblolly pine plantations. Considering economic significance, it has now become a rising concern among landowners, forest managers, and forest health state cooperators. However, the symptoms of the disease were perplexed somewhat with root disease(s) and recurrently attributed to invasive Phytophthora species due to the similarity of disease nature and devastation. Therefore, the study investigated the potential causal agent of this disease and characterized the fungi associated with loblolly pine needle defoliation in the southeastern USA. Besides, 70 trees were selected at seven long-term monitoring plots at Chatom, Alabama, to monitor and record the annual disease incidence and severity. Based on colony morphology and ITS-rDNA sequence data, a total of 28 species of fungi representing 17 families have been recovered from diseased loblolly pine needles. The native brown-spot pathogen, Lecanosticta acicola, was the species most frequently recovered from unhealthy loblolly pine needles in combination with some other common needle cast and rust pathogen(s). Identification was confirmed using morphological similarity and amplification of translation elongation factor 1-alpha gene region of interest. Tagged trees were consistently found chlorotic and defoliated from 2019 to 2020. The current emergence of the brown-spot pathogen causing loblolly pine mortality necessitates the investigation of the role of changing climatic conditions, which might be associated with increased pathogen pressure to loblolly pines in the southeastern USA.

Keywords: brown-spot needle blight, loblolly pine, needle defoliation, plantation forestry

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Authors: El Montassir Dahmane, Nadia Eladlani, Aziz Ouahrouch, Mohammed Rhazi, Moha Taourirte

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The present study was aimed to approximate the optimal conditions to chromium recovery from wastewater by nanoparticles and whiskers of chitosan. Chitosan with an average molecular weight of 63 kDa and a 96% deacetylation degree was prepared according to our previous study. Chromium recovery is influenced by different parameters. In our search, we determined the appropriate range of pH to form chitosan–Cr(III), nanoparticles Cr(III), and whiskers– Cr(III) complex. We studied also the influence of chromium concentration and the nature of chitosan-based materials on the complexation process. Our main aim is to approximate the optimal conditions to remove chromium(III) from the tanning bath, recuperated from tannery wastewater of Marrakech in Morocco. A Perkin Elmer optima 2000 Inductively Coupled Plasma- Optical Emission Spectrometer (ICP-OES), was used to determine the quantity of chromium persistent in tannery wastewater after complexation phenomenon. To the best of our knowledge, this is the first report interested in the optimal conditions for chromium recovery from wastewater by nanoparticles and whiskers of chitosan. From our research, we found that in chromium solution, the appropriate range of pH to form complex is between 5.6 and 6.7. Also, the complexation of Cr(III) is depending on the nature of complexing ligand and chromium concentration. The obtained results reveal that nanoparticles present an excellent adsorption capacity regardless of chromium concentration. In addition, after a critical chromium concentration (250 mg/l), our ligand becomes saturated, that requires an increase of ligand mass for increasing chromium concentration in order to have a better adsorption capacity. Hence, in the same conditions, we used chitosan, its nanoparticles, whiskers, and chitosan based films to remove Cr(III) from tannery wastewater. The pH of this effluent was around 6, and its chromium concentration was 300 mg/l. The results expose that the sequence of complexing ligand in the effluent is the same in chromium solution, determined via our previous study. However, the adsorbed quantity is less due to the presence of other metallic ions in tannery wastewater. We conclude that the best complexing ligand-based chitosan is chitosan nanoaprticles whether it’s in chromium solution or in tannery wastewater. Nanoparticles are the best complexing ligand after 24 h of contact nanoparticles can remove 70% of chromium from this tannery wastewater.

Keywords: nanoparticles, whiskers, chitosan, chromium

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Authors: S. S. Singh, A. Bhattacharya, S. Bhattacharya

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The eukaryotic exosome complex plays a pivotal role in RNA biogenesis, maturation, surveillance and differential expression of various RNAs in response to varying environmental signals. The exosome is composed of evolutionary conserved nine core subunits and the associated exonucleases Rrp6 and Rrp44. Rrp6p is crucial for the processing of rRNAs, other non-coding RNAs, regulation of polyA tail length and termination of transcription. Rrp6p, a 3’-5’ exonuclease is required for degradation of 5’-external transcribed spacer (ETS) released from the rRNA precursors during the early steps of pre-rRNA processing. In the parasitic protist Entamoeba histolytica in response to growth stress, there occurs the accumulation of unprocessed pre-rRNA and 5’ ETS sub fragment. To understand the processes leading to this accumulation, we looked for Rrp6 and the exosome subunits in E. histolytica, by in silico approaches. Of the nine core exosomal subunits, seven had high percentage of sequence similarity with the yeast and human. The EhRrp6 homolog contained exoribonuclease and HRDC domains like yeast but its N- terminus lacked the PMC2NT domain. EhRrp6 complemented the temperature sensitive phenotype of yeast rrp6Δ cells suggesting conservation of biological activity. We showed 3’-5’ exoribonuclease activity of EhRrp6p with in vitro-synthesized appropriate RNAs substrates. Like the yeast enzyme, EhRrp6p degraded unstructured RNA, but could degrade the stem-loops slowly. Furthermore, immunolocalization revealed that EhRrp6 was nuclear-localized in normal cells but was diminished from nucleus during serum starvation, which could explain the accumulation of 5’ETS during stress. Our study shows functional conservation of EhRrp6p in E.histolytica, an early-branching eukaryote, and will help to understand the evolution of exosomal components and their regulatory function.

Keywords: entamoeba histolytica, exosome complex, rRNA processing, Rrp6

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Authors: Abhilash Sahu, Amit Priyadarshi

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In this paper, we will discuss the existence of weak solutions of the Kirchhoff type boundary value problem on the Sierpinski gasket. Where S denotes the Sierpinski gasket in R² and S₀ is the intrinsic boundary of the Sierpinski gasket. M: R → R is a positive function and h: S × R → R is a suitable function which is a part of our main equation. ∆p denotes the p-Laplacian, where p > 1. First of all, we will define a weak solution for our problem and then we will show the existence of at least two solutions for the above problem under suitable conditions. There is no well-known concept of a generalized derivative of a function on a fractal domain. Recently, the notion of differential operators such as the Laplacian and the p-Laplacian on fractal domains has been defined. We recall the result first then we will address the above problem. In view of literature, Laplacian and p-Laplacian equations are studied extensively on regular domains (open connected domains) in contrast to fractal domains. In fractal domains, people have studied Laplacian equations more than p-Laplacian probably because in that case, the corresponding function space is reflexive and many minimax theorems which work for regular domains is applicable there which is not the case for the p-Laplacian. This motivates us to study equations involving p-Laplacian on the Sierpinski gasket. Problems on fractal domains lead to nonlinear models such as reaction-diffusion equations on fractals, problems on elastic fractal media and fluid flow through fractal regions etc. We have studied the above p-Laplacian equations on the Sierpinski gasket using fibering map technique on the Nehari manifold. Many authors have studied the Laplacian and p-Laplacian equations on regular domains using this Nehari manifold technique. In general Euler functional associated with such a problem is Frechet or Gateaux differentiable. So, a critical point becomes a solution to the problem. Also, the function space they consider is reflexive and hence we can extract a weakly convergent subsequence from a bounded sequence. But in our case neither the Euler functional is differentiable nor the function space is known to be reflexive. Overcoming these issues we are still able to prove the existence of at least two solutions of the given equation.

Keywords: Euler functional, p-Laplacian, p-energy, Sierpinski gasket, weak solution

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Authors: Balakrishna Shetty

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Introduction: Stem Cell Imaging is a challenging field since the advent of Stem Cell treatment in humans. Series of research on tagging and tracking the stem cells has not been very effective. The present study is an effort by the authors to track the stem cells injected into calf muscles by Magnetic Resonance Diffusion Weighted Imaging. Materials and methods: Stem Cell injection deep into the calf muscles of patients with peripheral vascular disease is one of the recent treatment modalities followed in our institution. 5 patients who underwent deep intramuscular injection of stem cells as treatment were included for this study. Pre and two hours Post injection MRI of bilateral calf regions was done using 1.5 T Philips Achieva, 16 channel system using 16 channel torso coils. Axial STIR, Axial Diffusion weighted images with b=0 and b=1000 values with back ground suppression (DWIBS sequence of Philips MR Imaging Systems) were obtained at 5 mm interval covering the entire calf. The invert images were obtained for better visualization. 120ml of autologous bone marrow derived stem cells were processed and enriched under c-GMP conditions and reduced to 40ml solution containing mixture of above stem cells. Approximately 40 to 50 injections, each containing 0.75ml of processed stem cells, was injected with marked grids over the calf region. Around 40 injections, each of 1ml normal saline, is injected into contralateral leg as control. Results: Significant Diffusion hyper intensity is noted at the site of injected stem cells. No hyper intensity noted before the injection and also in the control side where saline was injected conclusion: This is one of the earliest studies in literature showing diffusion hyper intensity in intramuscularly injected stem cells. The advantages and deficiencies in this study will be discussed during the presentation.

Keywords: stem cells, imaging, DWI, peripheral vascular disease

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Authors: M. L. Mangena, N. Mokoena, K. Rashamuse, M. G. Tlou

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Tertiary alcohol ester (TAE) hydrolases are a group of esterases (EC 3.1.1.-) that catalyze the kinetic resolution of TAEs and as a result, they are sought-after for the production of optically pure tertiary alcohols (TAs) which are useful as building blocks for number biologically active compounds. What sets these enzymes apart is, the presence of a GGG(A)X-motif in the active site which appears to be the main reason behind their activity towards the sterically demanding TAEs. The genome of Pseudomonas syringae pv. maculicola (Psm) comprises a multitude of genes that encode esterases. We therefore, hypothesize that some of these genes encode TAE hydrolases. In this study, Psm was screened for TAE hydrolase activity using the linalyl acetate (LA) plate assay and a positive reaction was observed. As a result, the genome of Psm was screened for esterases with a GGG(A)X-motif using the motif search tool and two potential TAE hydrolase genes (PsmEST1 and 2, 1100 and 1000bp, respectively) were identified, PsmEST1 was amplified by PCR and the gene sequenced for confirmation. Analysis of the sequence data with the SingnalP 4.1 server revealed that the protein comprises a signal peptide (22 amino acid residues) on the N-terminus. Primers specific for the gene encoding the mature protein (without the signal peptide) were designed such that they contain NdeI and XhoI restriction sites for directional cloning of the PCR products into pET28a. The gene was expressed in E. coli JM109 (DE3) and the clones screened for TAE hydrolase activity using the LA plate assay. A positive clone was selected, overexpressed and the protein purified using nickel affinity chromatography. The activity of the esterase towards LA was confirmed using thin layer chromatography.

Keywords: hydrolases, tertiary alcohol esters, tertiary alcohols, screening, Pseudomonas syringae pv., maculicola genome, esterase activity, linalyl acetate

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Authors: Mohammad Moridzadeh, Mohammad Djavid, Barry Doyle

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An assessment of the long-term stability of a cavern in Chagrin shale excavated by the sequential excavation method was performed during and after construction. During the excavation of the cavern, deformations of rock mass were measured at the surface of excavation and within the rock mass by surface and deep measurement instruments. Rock deformations were measured during construction which appeared to result from the as-built excavation sequence that had potentially disturbed the rock and its behavior. Also some additional time dependent rock deformations were observed during and post excavation. Several opinions have been expressed to explain this time dependent deformation including stress changes induced by excavation, strain softening (or creep) in the beddings with and without clay and creep of the shaley rock under compressive stresses. In order to analyze and replicate rock behavior observed during excavation, including current and post excavation elastic, plastic, and time dependent deformation, Finite Element Analysis (FEA) was performed. The analysis was also intended to estimate long term deformation of the rock mass around the excavation. Rock mass behavior including time dependent deformation was measured by means of rock surface convergence points, MPBXs, extended creep testing on the long anchors, and load history data from load cells attached to several long anchors. Direct creep testing of Chagrin Shale was performed on core samples from the wall of the Pump Room. Results of these measurements were used to calibrate the FEA of the excavation. These analyses incorporate time dependent constitutive modeling for the rock to evaluate the potential long term movement in the roof, walls, and invert of the cavern. The modeling was performed due to the concerns regarding the unanticipated behavior of the rock mass as well as the forecast of long term deformation and stability of rock around the excavation.

Keywords: Cavern, Chagrin shale, creep, finite element.

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Authors: Sundru Manjulata Devi, Prakash M. Halami

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The immemorial use of fermented foods from vegetables, dairy and other biological sources are of great demand in India because of their health benefits. However, the diversity of Lactobacillus plantarum group (LPG) of vegetable origin has not been revealed yet, particularly with reference to their probiotic functionalities. In the present study, the different species of probiotic Lactobacillus plantarum group (LPG) i.e., L. plantarum subsp. plantarum MTCC 5422 (from fermented cereals), L. plantarum subsp. argentoratensis FG16 (from fermented bamboo shoot) and L. paraplantarum MTCC 9483 (from fermented gundruk) (as characterized by multiplex recA PCR assay) were considered to investigate their relative expression of MUB domains of mub gene (mucin binding protein) by Real time PCR. Initially, the allelic variation in the mub gene was assessed and found to encode three different variants (Type I, II and III). All the three types had 8, 9 and 10 MUB domains respectively (as analysed by Pfam database) and were found to be responsible for adhesion of bacteria to the host intestinal epithelial cells. These domains either get inserted or deleted during speciation or evolutionary events and lead to divergence. The reverse transcriptase qPCR analysis with mubLPF1+R1 primer pair supported variation in amplicon sizes with 300, 500 and 700 bp among different LPG strains. The relative expression of these MUB domains significantly unregulated in the presence of 1% mucin in overnight grown cultures. Simultaneously, the mub gene expressed efficiently by 7 fold in the culture L. paraplantarum MTCC 9483 with 10 MUB domains. An increase in the expression levels for L. plantarum subsp. plantarum MTCC 5422 and L. plantarum subsp. argentoratensis FG16 (MCC 2974) with 9 and 8 repetitive domains was around 4 and 2 fold, respectively. The detection and expression of an integrase (int) gene in the upstream region of mub gene reveals the excision and integration of these repetitive domains. Concurrently, an in vitro adhesion assay to mucin and exclusion of pathogens (such as Listeria monocytogenes and Micrococcus leuteus) was investigated and observed that the L. paraplantarum MTCC 9483 with more adhesion domains has more ability to adhere to mucin and inhibited the growth of pathogens. The production and expression of plantaricin-like bacteriocin (plnNC8 type) in MTCC 9483 suggests the pathogen inhibition. Hence, the expression of MUB domains can act as potential biomarkers in the screening of a novel probiotic LPG strain with adherence property. The present study provides a platform for an easy, rapid, less time consuming, low-cost methodology for the detection of potential probiotic bacteria. It was known that the traditional practices followed in the preparation of fermented bamboo shoots/gundruk/cereals of Indian foods contain different kinds of neutraceuticals for functional food and novel compounds with health promoting factors. In future, a detailed study of these food products can add more nutritive value, consumption and suitable for commercialization.

Keywords: adhesion gene, fermented foods, MUB domains, probiotics

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Authors: Salma H. Abu Hafsa, A. Mendonca, B. Brehm-Stecher, A. A. Hassan, S. A. Ibrahim

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Enterococci are important inhabitants of the animal intestine and are widely used in probiotic products. A probiotic strain is expected to possess several desirable properties in order to exert beneficial effects. Therefore, the objective of this study was to isolate and characterize strains of Enterococcus sp. from chicken cecal and fecal samples to determine potential probiotic properties. Enterococci were isolated from thirty one chicken cecal and fecal samples collected from a local farm. In vitro studies were performed to assess antibacterial activity (using agar well diffusion and cell free supernatant broth technique against Salmonella enterica serotype Enteritidis), susceptibility to antibiotics (amoxycillin, cotrimoxazole, chloramphenicol, cefuroxime, ceftriaxone, ciprofloxacin, and nalidixic acid), survival in acidic conditions, resistance to bile salts, and their survival during simulated gastric juice conditions at pH 2.5. Isolates were identified using biochemical and molecular assays (API 50 CHL, and API ZYM kits followed by 16S rDNA gene sequence analysis). Two strains were identified, of which, Enteroccocus faecium was capable of inhibiting the growth of S. enteritidis and was susceptible to a wide range of antibiotics. In addition, the isolated strain exhibited significant resistance under highly acidic conditions (pH=2.5) for 8 hours and survived well in bile salt at 0.2% for 24 hours and showing ability to survive in the presence of simulated gastric juice at pH 2.5. Based on these results, the E. faecium isolate fulfills some of the criteria to be considered as a probiotic strain and therefore, could be used as a feed additive with good potential for controlling S. enteritidis in chickens. However, in vivo studies are needed to determine the safety of the strain.

Keywords: acid tolerance, antimicrobial activity, Enterococcus faecium, probiotic

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Authors: Ram Sharan Mehta, Gayanandra Malla, Anita Gurung, Anu Aryal, Divya Labh, Hricha Neupane

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Objectives: Lack of resuscitation skills of nurses and doctors in basic life support (BLS) and advanced life support (ALS) has been identified as a contributing factor to poor outcomes of cardiac arrest victims. The objective of this study was to examine retention of life support measures (BLS/ALS) knowledge and skills of nurses following education intervention programme. Materials and Methods: Pre-experimental research design was used to conduct the study among the nurses working in medical units of B.P Koirala Institute of Health Sciences, where CPR is very commonly performed. Using convenient sampling technique total of 20 nurses agreed to participate and give consent were included in the study. The theoretical, demonstration and re-demonstration were arranged involving the trained doctors and nurses during the three hours educational session. Post-test was carried out after two week of education intervention programme. The 2010 BLS & ALS guidelines were used as guide for the study contents. The collected data were analyzed using SPSS-15 software. Results: It was found that there is significant increase in knowledge after education intervention in the components of life support measures (BLS/ALS) i.e. ratio of chest compression to ventilation in BLS (P=0.001), correct sequence of CPR (p <0.001), rate of chest compression in ALS (P=0.001), the depth of chest compression in adult CPR (p<0.001), and position of chest compression in CPR (P=0.016). Nurses were well appreciated the programme and request to continue in future for all the nurses. Conclusions: At recent BLS/ALS courses (2010), a significant number of nurses remain without any such training. Action is needed to ensure all nurses receive BLS training and practice this skill regularly in order to retain their knowledge.

Keywords: pre-experimental, basic and advance life support, nurses, sampling technique

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Authors: Ali Kadivar, Kaveh Niayesh

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The integration of green energy resources is a major focus, and the role of Medium Voltage Direct Current (MVDC) systems is exponentially expanding. However, the protection of MVDC systems against DC faults is a challenge that can have consequences on reliable and safe grid operation. This challenge reveals the need for MVDC circuit breakers (MVDC CB), which are in infancies of their improvement. Therefore will be a lack of MVDC CBs standards, including thresholds for acceptable power losses and operation speed. To establish a baseline for comparison purposes, a benchmark system for testing future MVDC CBs is vital. The literatures just give the timing sequence of each switch and the emphasis is on the topology, without in-depth study on the control algorithm of DCCB, as the circuit breaker control system is not yet systematic. A digital testing benchmark is designed for the Proof-of-concept of simulation studies using software models. It can validate studies based on real-time digital simulators and Transient Network Analyzer (TNA) models. The proposed experimental setup utilizes data accusation from the accurate sensors installed on the tested MVDC CB and through general purpose input/outputs (GPIO) from the microcontroller and PC Prototype studies in the laboratory-based models utilizing Hardware-in-the-Loop (HIL) equipment connected to real-time digital simulators is achieved. The improved control algorithm of the circuit breaker can reduce the peak fault current and avoid arc resignation, helping the coordination of DCCB in relay protection. Moreover, several research gaps are identified regarding case studies and evaluation approaches.

Keywords: DC circuit breaker, hardware-in-the-loop, real time digital simulation, testing benchmark

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Authors: Boitumelo Setlhare, Mduduzi P. Mokoena, Ademola O. Olaniran

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Agricultural and industrial activities have led to increasing production of xenobiotics such as 2,4-dichlorophenol (2,4-DCP), a derivative of 2,4-dichlorophenoxyacetic acid (2,4-D), which is a widely used herbicide. Bioremediation offers an efficient, cost-effective and environmentally friendly method for degradation of the compound through the activities of the various microbial enzymes involved in the catabolic pathway. The aim of this study was to isolate and characterize bacterial isolate indigenous to contaminated sites in Durban, South Africa for 2,4-DCP degradation. One bacterium capable of utilizing 2,4-DCP as sole carbon source was isolated using culture enrichment technique and identified as Pseudomonas chlororaphis strain UFB2 via PCR amplification and analysis of 16S rRNA gene sequence. This isolate was able to degrade up to 75.11% of 2,4-DCP in batch cultures within 10 days, with the degradation rate constant of 0.14 mg/l/d. Phylogenetic analysis revealed the relatedness of this bacterial isolate to other Pseudomonas sp. previously characterized for chlorophenol degradation. PCR amplification of the catabolic genes involved in 2,4-DCP degradation revealed the presence of the correct amplicons for phenol hydroxylase (600 bp), catechol 1,2-dioxygenase (214 bp), muconate isomerase (851 bp), cis-dienelactone hydrolase (577 bp), and trans-dienelactone hydrolase (491 bp) genes. Enzyme assays revealed activity as high as 21840 mU/mg, 15630 mU/mg, 2340 mU/mg and 1490 mU/mg obtained for phenol hydroxylase, catechol 1,2-dioxygenase, cis-dienelactone hydroxylase and trans-dienelactone hydroxylase, respectively. The absence of catechol 2,3-dioxygenase gene and the corresponding enzyme in this isolate suggests that the organism followed ortho-pathway for 2,4-DCP degradation. Furthermore, the absence of malaycetate reductase genes showed that the bacterium may not be able to completely mineralize 2,4-DCP. Further studies are required to optimize 2,4-DCP degradation by this isolate as well as to elucidate the mechanism of 2,4-DCP degradation.

Keywords: biodegradation, catechol 1, 2-dioxygenase, 2, 4-dichlorophenol, phenol hydroxylase, Pseudomonas chlororaphis

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Authors: Vincent Murray

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The glycopeptide bleomycin is used in the treatment of testicular cancer, Hodgkin's lymphoma, and squamous cell carcinoma. Bleomycin damages and cleaves DNA in human cells, and this is considered to be the main mode of action for bleomycin's anti-tumor activity. In particular, double-strand breaks are thought to be the main mechanism for the cellular toxicity of bleomycin. Using Illumina next-generation DNA sequencing techniques, the genome-wide sequence specificity of bleomycin-induced double-strand breaks was determined in human cells. The degree of bleomycin cleavage was also assessed at the transcription start sites (TSSs) of actively transcribed genes and compared with non-transcribed genes. It was observed that bleomycin preferentially cleaved at the TSSs of actively transcribed human genes. There was a correlation between the degree of this enhanced cleavage at TSSs and the level of transcriptional activity. Bleomycin cleavage is also affected by chromatin structure and at TSSs, the peaks of bleomycin cleavage were approximately 200 bp apart. This indicated that bleomycin was able to detect phased nucleosomes at the TSSs of actively transcribed human genes. The genome-wide cleavage pattern of the bleomycin analogues 6′-deoxy-BLM Z and zorbamycin was also investigated in human cells. As found for bleomycin, these bleomycin analogues also preferentially cleaved at the TSSs of actively transcribed human genes. The cytotoxicity (IC₅₀ values) of these bleomycin analogues was determined. It was found that the degree of enhanced cleavage at TSSs was inversely correlated with the IC₅₀ values of the bleomycin analogues. This suggested that the level of cleavage at the TSSs of actively transcribed human genes was important for the cytotoxicity of bleomycin and analogues. Hence this study provided a deeper understanding of the cellular processes involved in the cancer chemotherapeutic activity of bleomycin.

Keywords: anti-tumour activity, bleomycin analogues, chromatin structure, genome-wide study, Illumina DNA sequencing

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Authors: M. A. Barros, M. V. Barros

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The aim of this work is to analyze the discursive dynamics of preservice teachers during the implementation of a didactic sequence on topics of Quantum Mechanics for High School. Our research methodology was qualitative, case study type, in which we selected two prospective teachers on the Physics Teacher Training Course of the Sao Carlos Institute of Physics, at the University of Sao Paulo/Brazil. The set of modes of communication analyzed were the intentions and interventions of the teachers, the established communicative approach, the patterns and the contents of the interactions between teachers and students. Data were collected through video recording, interviews and questionnaires conducted before and after an 8 hour mini-course, which was offered to a group of 20 secondary students. As teaching strategy we used an active learning methodology, called: Peer Instruction. The episodes pointed out that both future teachers used interactive dialogic and authoritative communicative approaches to mediate the discussion between peers. In the interactive dialogic dimension the communication pattern was predominantly I-R-F (initiation-response-feedback), in which the future teachers assisted the students in the discussion by providing feedback to their initiations and contributing to the progress of the discussions between peers. Although the interactive dialogic dimension has been preferential during the use of the Peer Instruction method the authoritative communicative approach was also employed. In the authoritative dimension, future teachers used predominantly the type I-R-E (initiation-response-evaluation) communication pattern by asking the students several questions and leading them to the correct answer. Among the main implications the work contributes to the improvement of the practices of future teachers involved in applying active learning methodologies in classroom by identifying the types of communicative approaches and communication patterns used, as well as researches on curriculum innovation in physics in high school.

Keywords: curricular innovation, high school, physics teaching, discursive dynamics

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Authors: Priya Varma, Denis John McKeown

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Psychological time, unlike physical time, is believed to be ‘compressive’ in the sense that the mental representations of a series of events may be internally arranged with ever decreasing inter-event spacing (looking back from the most recently encoded event). If this is true, the record within immediate memory of recent events is severely temporally distorted. Although this notion of temporal distortion of the memory record is captured within some theoretical accounts of human forgetting, notably temporal distinctiveness accounts, the way in which the fundamental nature of the distortion underpins memory and forgetting broadly is barely recognised or at least directly investigated. Our intention here was to manipulate the spacing of items for recall in order to ‘reverse’ this supposed natural compression within the encoding of the items. In Experiment 1 three schedules of presentation (expanding, contracting and fixed irregular temporal spacing) were created using logarithmic spacing of the words for both free and serial recall conditions. The results of recall of lists of 7 words showed statistically significant benefits of temporal isolation, and more excitingly the contracting word series (which we may think of as reversing the natural compression within the mental representation of the word list) showed best performance. Experiment 2 tested for effects of active verbal rehearsal in the recall task; this reduced but did not remove the benefits of our temporal scheduling manipulation. Finally, a third experiment used the same design but with Chinese characters as memoranda, in a further attempt to subvert possible verbal maintenance of items. One change to the design here was to introduce a probe item following the sequence of items and record response times to this probe. Together the outcomes of the experiments broadly support the notion of temporal compression within immediate memory.

Keywords: memory, serial position curves, temporal isolation, temporal schedules

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Authors: Tae-Hoon Kim, Kwon-Ha Yoon, Hong Young Jun, Ki-Jong Kim, Young Hwan Lee, Myeung Su Lee, Keum Ha Choi, Ki Jung Yun, Eun Young Cho, Yong-Yeon Jeong, Chung-Hwan Jun

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Purpose: To assess the changes of hepatic metabolite for differentiation between non-alcoholic steatohepatitis (NASH) and simple steatosis on proton magnetic resonance spectroscopy (1H-MRS) in both humans and animal model. Methods: The local institutional review board approved this study and subjects gave written informed consent. 1H-MRS measurements were performed on a localized voxel of the liver using a point-resolved spectroscopy (PRESS) sequence and hepatic metabolites of alanine (Ala), lactate/triglyceride (Lac/TG), and TG were analyzed in NASH, simple steatosis and control groups. The group difference was tested with the ANOVA and Tukey’s post-hoc tests, and diagnostic accuracy was tested by calculating the area under the receiver operating characteristics (ROC) curve. The associations between metabolic concentration and pathologic grades or non-alcoholic fatty liver disease(NAFLD) activity scores were assessed by the Pearson’s correlation. Results: Patient with NASH showed the elevated Ala(p<0.001), Lac/TG(p < 0.001), TG(p < 0.05) concentration when compared with patients who had simple steatosis and healthy controls. The NASH patients were higher levels in Ala(mean±SEM, 52.5±8.3 vs 2.0±0.9; p < 0.001), Lac/TG(824.0±168.2 vs 394.1±89.8; p < 0.05) than simple steatosis. The area under the ROC curve to distinguish NASH from simple steatosis was 1.00 (95% confidence interval; 1.00, 1.00) with Ala and 0.782 (95% confidence interval; 0.61, 0.96) with Lac/TG. The Ala and Lac/TG levels were well correlated with steatosis grade, lobular inflammation, and NAFLD activity scores. The metabolic changes in human were reproducible to a mice model induced by streptozotocin injection and a high-fat diet. Conclusion: 1H-MRS would be useful for differentiation of patients with NASH and simple hepatic steatosis.

Keywords: non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, 1H MR spectroscopy, hepatic metabolites

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Authors: Sharique Ahmed, Khushtar Anwar Salman

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Alpha-1-antitrypsin (AAT) is a major plasma serine protease inhibitor (SERPIN). Hereditary AAT deficiency is one of the common diseases in some part of the world. AAT is mainly produced in the liver and functions to protect the lung against proteolytic damage (e.g., from neutrophil elastase) acting as the major inhibitor for neutrophil elastase. α (1)-Antitrypsin (AAT) deficiency is an under recognized genetic condition that affects approximately 1 in 2,000 to 1 in 5,000 individuals and predisposes to liver disease and early-onset emphysema. Not only does α-1-antitrypsin deficiency lead to disabling syndrome of pulmonary emphysema, there are other disorders too which include ANCA (antineutrophilic cytoplasmic antibody) positive Wegener's granulomatosis, diffuse bronchiectasis, necrotizing panniculitis in α-1-antitrypsin phenotype (S), idiopathic pulmonary fibrosis and steroid dependent asthma. Augmentation therapy with alpha-1 antitrypsin (AAT) from human plasma has been available for specific treatment of emphysema due to AAT deficiency. Apart from this several observations have also suggested a role for endogenous suppressors of HIV-1, alpha-1 antitrypsin (AAT) has been identified to be one of those. In view of its varied important role in humans, serum from a mammalian source was chosen for the isolation and purification. Studies were performed on the homogeneous fraction. This study suggests that the buffalo serum α-1-antritrypsin has characteristics close to ovine, dog, horse and more importantly to human α-1-antritrypsin in terms of its hydrodynamic properties such as molecular weight, carbohydrate content, etc. The similarities in the hydrodynamic properties of buffalo serum α-1-antitrypsin with other sources of mammalian α-1-antitrypsin mean that it can be further studied and be a potential source for "augmentation therapy", as well as a source of AAT replacement therapy to raise serum levels above the protective threshold. Other parameters like the amino acid sequence, the effect of denaturants, and the thermolability or thermostability of the inhibitor will be the interesting basis of future studies on buffalo serum alpha-1 antitrypsin (AAT).

Keywords: α-1-antitrypsin, augmentation therapy , hydrodynamic properties, serine protease inhibitor

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Authors: Andrzej Wałęga, Marta Cebulska, Agnieszka Ziernicka-Wojtaszek, Wojciech Młocek, Agnieszka Wałęga, Tommaso Caloiero

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Drought is one of the natural phenomena influencing many aspects of human activities like food production, agriculture, industry, and the ecological conditions of the environment. In the area of the Polish Carpathians, there are periods with a deficit of rainwater and an increasing frequency in dry months, especially in the cold half of the year. The aim of this work is a spatial and temporal analysis of drought, expressed as SPI in a heterogenous area of the Polish Carpathian and of the highland Region in the Central part of Europe based on long-term precipitation data. Also, to our best knowledge, for the first time in this work, drought characteristics analyzed via the SPI were discussed based on the atmospheric circulation calendar. The study region is the Upper Vistula Basin, located in the southern and south-eastern part of Poland. In this work, monthly precipitation from 56 rainfall stations was analysed from 1961 to 2022. The 3-, 6-, 9-, and 12-month Standardized Precipitation Index (SPI) were used as indicators of meteorological drought. For the 3-month SPI, the main climatic mechanisms determining extreme droughts were defined based on the calendar of synoptic circulations. The Mann-Kendall test was used to detect the trend of extreme droughts. Statistically significant trends of SPI were observed on 52.7% of all analyzed stations, and in most cases, a positive trend was observed. Statistically significant trends were more frequently observed in stations located in the western part of the analyzed region. Long-term droughts, represented by the 12-month SPI, occurred in all stations but not in all years. Short-term droughts (3-month SPI) were most frequent in the winter season, 6 and 9-month SPI in winter and spring, and 12-month SPI in winter and autumn, respectively. The spatial distribution of drought was highly diverse. The most intensive drought occurred in 1984, with the 6-month SPI covering 98% of the analyzed region and the 9 and 12-month SPI covering 90% of the entire region. Droughts exhibit a seasonal pattern, with a dominant 10-year periodicity for all analyzed variants of SPI. Additionally, Fourier analysis revealed a 2-year periodicity for the 3-, 6-, and 9-month SPI and a 31-year periodicity for the 12-month SPI. The results provide insights into the typical climatic conditions in Poland, with strong seasonality in precipitation. The study highlighted that short-term extreme droughts, represented by the 3-month SPI, are often caused by anticyclonic situations with high-pressure wedges Ka and Wa, and anticyclonic West as observed in 52.3% of cases. These findings are crucial for understanding the spatial and temporal variability of short and long-term extreme droughts in Central Europe, particularly for the agriculture sector dominant in the northern part of the analyzed region, where drought frequency is highest.

Keywords: atmospheric circulation, drought, precipitation, SPI, the Upper Vistula Basin

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Authors: Yang Ye, Hongfei Qiu, Yaqi Li

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The planning and construction of traditional cities are oriented by cars, which leads to the problems of insufficient urban public space, fragmentation, and low utilization efficiency. With the development of driverless technology, the urban structure will change from the traditional single-core grid structure to the multi-core model. In terms of traffic organization, with the release of land for traffic facilities, public space will become more continuous and integrated with traffic space. In the context of driverless technology, urban public reconstruction is characterized by modularization and high efficiency, and its planning and layout features accord with points (service facilities), lines (smart lines), surfaces (activity centers). The public space of driverless urban roads will provide diversified urban public facilities and services. The intensive urban layout makes the commercial public space realize the functions of central activities and style display, respectively, in the interior (building atrium) and the exterior (building periphery). In addition to recreation function, urban green space can also utilize underground parking space to realize efficient dispatching of shared cars. The roads inside the residential community will be integrated into the urban landscape, providing conditions for the community public activity space with changing time sequence and improving the efficiency of space utilization. The intervention of driverless technology will change the thinking of traditional urban construction and turn it into a human-oriented one. As a result, urban public space will be richer, more connected, more efficient, and the urban space justice will be optimized. By summarizing the frontier research, this paper discusses the impact of unmanned driving on cities, especially urban public space, which is beneficial for landscape architects to cope with the future development and changes of the industry and provides a reference for the related research and practice.

Keywords: driverless, urban public space, construction strategy, urban design

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Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

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Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

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Authors: Alejandro Arnaldo Barroso Martinez

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Unlike sex, which is constituted by anatomic-physiological differences, gender is a social construction. Our thoughts and behaviors as females and males are not etched in stone by our biology but rather from how society expects us to think and behave based on our sex assignment in the womb. Social expectations, values, and roles are taken on by individuals and shape the ways considered acceptable and linked to our bodies, feelings, and interpersonal relationships. Furthermore, these evolve into dire consequences for those who do not meet these disciplinary, economic, and cultural standards. Then, the social learning of gender identity implies the individual’s psychological sense of being, and it might be highly linked to a sense of life and suicide attempts. As a result, suicide has been considered a gender issue with differences in the rates and means used by men and women worldwide. Nevertheless, there has been a misunderstanding of the meaning of being male or female in a particular context and how it becomes a risk process for suicide attempts. For this reason, the general objective of the current research is to explain how this process occurs in Cuba. From a Critical Sociology and Social Psychology, a qualitative methodology was developed through six case studies and qualitative in-depth interviews. The analysis is focused on the sequence and interplay between two dimensions of meaning: signifiers and voices. Findings show that the risk process of suicide attempts in Cuba means some patriarchal beliefs and practices as part of informal educational models and some positivist practices in mental health attention. Findings also show that community relations create a sense of belonging, and it is a protection against suicide attempts in Cuba. Those frames of signifiers and voices explain in both males and females but differently when and how they are suffering from isolation, violence, the normalization of emotional awareness, and emotional distress expression. Suicide prevention programs should take gender learning into account as a cultural process.

Keywords: social constructions, gender identity, meanings, suicide attempt

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Authors: Chingwen Yeh, I. Chen Huang

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This paper aims to conduct a case study on kinesthetic intelligence development intervention with a child who has Asperger symptom identified by physician. First, the characteristics of Asperger were defined based on the related literature. Some Asperger's people are born with outstanding insight and are good at solving complex and difficult problems. In contrast to high-functioning autistic, Asperger children do not lose their ability to express themselves verbally. However in the cognitive function, they focus mainly on the things they are interested in instead of paying attention to the whole surrounding situation. Thus it is difficult for them not only to focus on things that they are not interesting in, but also to interact with people. Secondly, 8-weeks of kinesthetic intelligence development courses were designed within a series of physical action that including the following sections: limbs coordination, various parts of body rhythm changes, strength and space awareness and breathing practice. In classroom observations were recorded both on words and with video as the qualitative research data. Finally, in-depth interview with the case child’s teachers, parents and other in class observers were documented on a weekly base in order to examine the effectiveness of before and after the kinesthetic intelligence development course and to testify the usefulness of the lesson plan. This research found that the case child has improved significantly in terms of attention span and body movement creativity. In the beginning of intervention, the case child made less eyes contact with others. The instructor needed to face the case child to confirm the eyes contact. And the instructor also used various adjective words as guiding language for all kinds of movement sequence practice. The result can cause the case child’s attention and learning motivation. And the case child understand what to do to enhance kinesthetic intelligence. These authors hope findings of this study can contribute as reference for the further research on the related topic.

Keywords: asperger symptom, body rhythm, kinesthetic intelligence, space awareness

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

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

Keywords: emerging pathogens, Iran, juglans regia, MLSA

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Authors: Marcin Debowski, Marcin Zielinski, Miroslaw Krzemieniewski, Agata Glowacka-Gil, Paulina Rusanowska, Magdalena Zielinska, Agnieszka Cydzik-Kwiatkowska

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Technologies of biogas upgrading are now perceived as competitive solution combustion and production of electricity and heat. Biomethane production will ensure broader application as energy carrier than biogas. Biomethane can be used as fuel in internal combustion engines or introduced into the natural gas transmission network. Therefore, there is a need to search for innovative, economically and technically justified methods for biogas enrichment. The aim of this paper is to present a technology solution for biogas upgrading with immobilized algae biomass. Reactor for biogas upgrading with immobilized algae biomass can be used for removing CO₂ from the biogas, flue gases and the waste gases especially coming from different industry sectors, e.g. from the food industry from yeast production process, biogas production systems, liquid and gaseous fuels combustion systems, hydrocarbon processing technology. The basis for the technological assumptions of presented technology were laboratory works and analyses that tested technological variants of biogas upgrading. The enrichment of biogas with a methane content of 90-97% pointed to technological assumptions for installation on a technical scale. Reactor for biogas upgrading with algae biomass is characterized by a significantly lower cubature in relation to the currently used solutions which use CO₂ removal processes. The invention, by its structure, assumes achieving a very high concentration of biomass of algae through its immobilization in capsules. This eliminates the phenomenon of lowering the pH value, i.e. acidification of the environment in which algae grow, resulting from the introduction of waste gases at a high CO₂ concentration. The system for introducing light into algae capsules is characterized by a higher degree of its use, due to lower losses resulting from the phenomenon of absorption of light energy by water. The light from the light source is continuously supplied to the formed biomass of algae or cyanobacteria in capsules by the light tubes. The light source may be sunlight or a light generator of a different wavelength of light from 300 nm to 800 nm. A portion of gas containing CO₂, accumulated in the tank and conveyed by the pump is periodically introduced into the housing of the photobioreactor tank. When conveying the gas that contains CO₂, it penetrates the algal biomass in capsules through the outer envelope, displacing, from the algal biomass, gaseous metabolic products which are discharged by the outlet duct for gases. It contributes to eliminating the negative impact of this factor on CO₂ binding processes. As a result of the cyclic dosing of gases containing carbon dioxide, gaseous metabolic products of algae are displaced and removed outside the technological system. Technology for biogas upgrading with immobilized algae biomass is suitable for the small biogas plant. The advantages of this technology are high efficiency as well as useful algae biomass which can be used mainly as animal feed, fertilizers and in the power industry. The construction of the device allows effective removal of carbon dioxide from gases at a high CO₂ concentration.

Keywords: biogas, carbon dioxide, immobilised biomass, microalgae, upgrading

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Authors: Shringika Soni, Utkarsh Jain, Nidhi Chauhan

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Aptamers are recently discovered ~80-100 bp long artificial oligonucleotides that not only demonstrated their applications in therapeutics; it is tremendously used in diagnostic and sensing application to detect different biomarkers and drugs. Synthesizing aptamers for proteins or genomic template is comparatively feasible in laboratory, but drugs or other chemical target based aptamers require major specification and proper optimization and validation. One has to optimize all selection, amplification, and characterization steps of the end product, which is extremely time-consuming. Therefore, we performed asymmetric PCR (polymerase chain reaction) for random oligonucleotides pool synthesis, and further use them in Systematic evolution of ligands by exponential enrichment (SELEX) for anti-psychotic drugs based aptamers synthesis. Anti-psychotic drugs are major tranquilizers to control psychosis for proper cognitive functions. Though their low medical use, their misuse may lead to severe medical condition as addiction and can promote crime in social and economical impact. In this work, we have approached the in-vitro SELEX method for ssDNA synthesis for anti-psychotic drugs (in this case ‘target’) based aptamer synthesis. The study was performed in three stages, where first stage included synthesis of random oligonucleotides pool via asymmetric PCR where end product was analyzed with electrophoresis and purified for further stages. The purified oligonucleotide pool was incubated in SELEX buffer, and further partition was performed in the next stage to obtain target specific aptamers. The isolated oligonucleotides are characterized and quantified after each round of partition, and significant results were obtained. After the repetitive partition and amplification steps of target-specific oligonucleotides, final stage included sequencing of end product. We can confirm the specific sequence for anti-psychoactive drugs, which will be further used in diagnostic application in clinical and forensic set-up.

Keywords: anti-psychotic drugs, aptamer, biosensor, ssDNA, SELEX

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Authors: Zintle Kolo, Ndiko Ludidi

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The enzymatic activity of p-coumarate 3-hydroxylase (C3H) synthesize caffeic acid from p-coumaric acid. We recently showed that exogenously applied caffeic acid confers salinity tolerance in soybean (Glycine max) by inducing antioxidant enzymatic activity to promote enhanced scavenging or reactive oxygen species, thus limiting salinity-induced oxidative stress. Recent evidence also establishes that pre-treatment of plants with exogenously supplied caffeic acid improves plant tolerance to osmotic stress by improving plant antioxidant capacity and enhancing biosynthesis of compatible solutes. We aimed to identify a C3H in maize (Zea mays) and evaluate the effect of drought on the spatial and temporal expression of the gene encoding the candidate maize C3H (ZmC3H). Primary sequence analysis shows that ZmC3H shares 71% identity with an Arabidopsis thaliana C3H that is implicated in the control of Arabidopsis cell expansion, growth, and responses to stress. In silico ZmC3H promoter analysis reveals the presence of cis-acting elements that interact with transcription factors implicated in plant responses to drought. Spatial expression analysis by semi-quantitative RT-PCR shows that ZmC3H is expressed in both leaves and roots under normal conditions. However, drought represses the expression of ZmC3H in leaves whereas it up-regulates its expression in roots. These changes in ZmC3H expression correlate with the changes in the content of caffeic acid in maize in response to drought. We illustrate the implications of these changes in the expression of the gene in relation to maize responses to drought and discuss the potential of regulating caffeic acid biosynthesis towards genetic improvement of maize tolerance to drought stress. These findings have implications for food security because of the potential of the implications of the study for drought tolerance in maize.

Keywords: caffeic acid, drought-responsive expression, maize drought tolerance, p-coumarate 3-hydroxylase

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Authors: Eszter Repasi, Akos Koller

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Our genetic information determines our look, physiology, sports performance and all our features. Maximizing the performances of athletes have adopted a science-based approach to the nutritional support. Nowadays genetics studies have blended with nutritional sciences, and a dynamically evolving, new research field have appeared. Nutritional genomics is needed to be used by nutritional experts. This is a recent field of nutritional science, which can provide a solution to reach the best sport performance using correlations between the athlete’s genome, nutritions, molecules, included human microbiome (links between food, microbiome and epigenetics), nutrigenomics and nutrigenetics. Nutritional genomics has a tremendous potential to change the future of dietary guidelines and personal recommendations. Experts need to use new technology to get information about the athletes, like nutritional genomics profile (included the determination of the oral and gut microbiome and DNA coded reaction for food components), which can modify the preparation term and sports performance. The influence of nutrients on the genes expression is called Nutrigenomics. The heterogeneous response of gene variants to nutrients, dietary components is called Nutrigenetics. The human microbiome plays a critical role in the state of health and well-being, and there are more links between food or nutrition and the human microbiome composition, which can develop diseases and epigenetic changes as well. A nutritional genomics-based profile of athletes can be the best technic for a dietitian to make a unique sports nutrition diet plan. Using functional food and the right food components can be effected on health state, thus sports performance. Scientists need to determine the best response, due to the effect of nutrients on health, through altering genome promote metabolites and result changes in physiology. Nutritional biochemistry explains why polymorphisms in genes for the absorption, circulation, or metabolism of essential nutrients (such as n-3 polyunsaturated fatty acids or epigallocatechin-3-gallate), would affect the efficacy of that nutrient. Controlled nutritional deficiencies and failures, prevented the change of health state or a newly discovered food intolerance are observed by a proper medical team, can support better sports performance. It is important that the dietetics profession informed on gene-diet interactions, that may be leading to optimal health, reduced risk of injury or disease. A special medical application for documentation and monitoring of data of health state and risk factors can uphold and warn the medical team for an early action and help to be able to do a proper health service in time. This model can set up a personalized nutrition advice from the status control, through the recovery, to the monitoring. But more studies are needed to understand the mechanisms and to be able to change the composition of the microbiome, environmental and genetic risk factors in cases of athletes.

Keywords: gene-diet interaction, multidisciplinary team, microbiome, diet plan

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Authors: J. U. Santhosh Kumar, V. Krishna, Sebin Sebastian, G. S. Seethapathy, G. Ravikanth, R. Uma Shaanker

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Food is one of the basic needs of human beings. It requires the normal function of the body part and a healthy growth. Recently, food adulteration increases day by day to increase the quantity and make more benefit. Animal source foods can provide a variety of micronutrients that are difficult to obtain in adequate quantities from plant source foods alone. Particularly in the meat industry, products from animals are susceptible targets for fraudulent labeling due to the economic profit that results from selling cheaper meat as meat from more profitable and desirable species. This work presents an overview of the main PCR-based techniques applied to date to verify the authenticity of beef meat and meat products from beef species. We were analyzed 25 market beef samples in South India. We examined PCR methods based on the sequence of the cytochrome b gene for source species identification. We found all sample were sold as beef meat as Bos Taurus. However, interestingly Male meats are more valuable high price compare to female meat, due to this reason most of the markets samples are susceptible. We were used sex determination gene of cattle like TSPY(Y-encoded, testis-specific protein TSPY is a Y-specific gene). TSPY homologs exist in several mammalian species, including humans, horses, and cattle. This gene is Y coded testis protein genes, which only amplify the male. We used multiple PCR products form species-specific “fingerprints” on gel electrophoresis, which may be useful for meat authentication. Amplicons were obtained only by the Cattle -specific PCR. We found 13 market meat samples sold as female beef samples. These results suggest that the species-specific PCR methods established in this study would be useful for simple and easy detection of adulteration of meat products.

Keywords: authentication, meat products, species-specific, TSPY

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