Search results for: massively parallel sequencing

Authors: Il Ho Park, Joong Seob Lee, Sung Hun Kang, Jae-Min Shin, Il Seok Park, Seok Min Hong, Seok Jin Hong

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Introduction: The human microbiota is the aggregate of microorganisms, and the bacterial microbiome of the human digestive tract contributes to both health and disease. In health, bacteria are key components in the development of mucosal barrier function and in innate and adaptive immune responses, and they also work to suppress the establishment of pathogens. In human upper airway, the sinonasal microbiota might play an important role in chronic rhinosinusitis (CRS). The purpose of this study is to investigate the human upper airway microbiome in CRS patients and to compare the sinonasal microbiome of adults with children. Materials and methods: A total of 19 samples from 19 patients (Group1; 9 CRS in children, aged 5 to 14 years versus Group 2; 10 CRS in adults aged 21 to 59 years) were examined. Swabs were collected from the middle meatus and/or anterior ethmoid region under general anesthesia during endoscopic sinus surgery or tonsillectomy. After DNA extraction from swab samples, we analysed bacterial microbiome consortia using 16s rRNA gene sequencing approach (the Illumina MiSeq platform). Results: In this study, relatively abundance of the six bacterial phyla and tremendous genus and species found in substantial amounts in the individual sinus swab samples, include Corynebacterium, Hemophilus, Moraxella, and Streptococcus species. Anaerobes like Fusobacterium and Bacteroides were abundantly present in the children group, Bacteroides and Propionibacterium were present in adults group. In genus, Haemophilus was the most common CRS microbiome in children and Corynebacterium was the most common CRS microbiome in adults. Conclusions: Our results show the diversity of human upper airway microbiome, and the findings will suggest that CRS is a polymicrobial infection. The Corynebacterium and Hemophilus may live as commensals on mucosal surfaces of sinus in the upper respiratory tract. The further study will be needed for analysis of microbiome-human interactions in upper airway and CRS.

Keywords: microbiome, upper airway, chronic rhinosinusitis, adult and children

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Authors: Nonhlanhla Nkosi, Kulsum Kondiah

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The toxicological manifestation of heavy metals motivates interest towards the development of a reliable, eco-friendly biosorption process. With that being said, the aim of the current study was to characterise the EPS from heavy-metal resistant bacteria isolated from acid mine decant on the West Rand, Gauteng, South Africa. To achieve this, six exopolysaccharide (EPS) producing, metal resistant strains (Pb101, Pb102, Pb103, Pb204, Co101, and Ni101) were identified as Bacillus safensis strain NBRC 100820, Bacillus proteolyticus, Micrococcus luteus, Enterobacter sp. Pb204, Bacillus wiedmannii and Bacillus zhangzhouensis, respectively with 16S rRNA sequencing. Thereafter, EPS was extracted using chemical (formaldehyde/NaOH) and physical (ultrasonification) methods followed by physicochemical characterisation of carbohydrate, DNA, and protein contents using chemical assays and spectroscopy (FTIR- Fourier transformed infrared and 3DEEM- three-dimensional excitation-emission matrix fluorescence spectroscopy). EPS treated with formaldehyde/NaOH showed better recovery of macromolecules than ultrasonification. The results of the present study showed that carbohydrates were more abundant than proteins, with carbohydrate and protein concentrations of 8.00 mg/ml and 0.22 mg/ml using chemical method in contrast to 5.00 mg/ml and 0.77 mg/ml using physical method, respectively. The FTIR spectroscopy results revealed that the extracted EPS contained hydroxyl, amide, acyl, and carboxyl groups that corresponded to the aforementioned chemical analysis results, thus asserting the presence of carbohydrates, DNA, polysaccharides, and proteins in the EPS. These findings suggest that identified functional groups of EPS form surface charges, which serve as the binding sites for suspended particles, thus possibly mediating adsorption of divalent cations and heavy metals. Using the extracted EPS in the development of a cost-effective biosorption solution for industrial wastewater treatment is attainable.

Keywords: biosorbent, exopolysaccharides, heavy metals, wastewater treatment

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Authors: Daniel Aberdam

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Haploinsufficiency of PAX6 in humans is the main cause of congenital aniridia, a rare eye disease characterized by reduced visual acuity. Patients have also progressive disorders including cataract, glaucoma and corneal abnormalities making their condition very challenging to manage. Aniridia-related keratopathy (ARK), caused by a combination of factors including limbal stem-cell deficiency, impaired healing response, abnormal differentiation, and infiltration of conjunctival cells onto the corneal surface, affects up to 95% of patients. It usually begins in the first decade of life resulting in recurrent corneal erosions, sub-epithelial fibrosis with corneal decompensation and opacification. Unfortunately, current treatment options for aniridia patients are currently limited. Although animal models partially recapitulate this disease, there is no in vitro cellular model of AKT needed for drug/therapeutic tools screening and validation. We used genome editing (CRISPR/Cas9 technology) to introduce a nonsense mutation found in patients into one allele of the PAX6 gene into limbal stem cells. Resulting mutated clones, expressing half of the amount of PAX6 protein and thus representative of haploinsufficiency were further characterized. Sequencing analysis showed that no off-target mutations were induced. The mutated cells displayed reduced cell proliferation and cell migration but enhanced cell adhesion. Known PAX6 targets expression was also reduced. Remarkably, addition of soluble recombinant PAX6 protein into the culture medium was sufficient to activate endogenous PAX6 gene and, as a consequence, rescue the phenotype. It strongly suggests that our in vitro model recapitulates well the epithelial defect and becomes a powerful tool to identify drugs that could rescue the corneal defect in patients. Furthermore, we demonstrate that the homeotic transcription factor Pax6 is able to be uptake naturally by recipient cells to function into the nucleus.

Keywords: Pax6, crispr/cas9, limbal stem cells, aniridia, gene therapy

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Authors: Zuliani Mahmood, Thirumulu Ponnuraj Kannan, Yean Yean Chan, Salahddin A. Al-Hudhairy

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Caries is the most common childhood disease which develops due to disturbances in the physiological equilibrium in the dental plaque resulting in demineralization of tooth structures. Plaque and dentine samples were collected from three different tooth surfaces representing caries progression (intact, over carious lesion and dentine) in children with early childhood caries (ECC, n=36). In caries free (CF) children, plaque samples were collected from sound tooth surfaces at baseline and after one year (n=12). The genomic DNA was extracted from all samples and subjected to 16S rRNA PCR amplification. The end products were cloned into pCR®2.1-TOPO® Vector. Five randomly selected positive clones collected from each surface were sent for sequencing. Identification of the bacterial clones was performed using BLAST against GenBank database. In the ECC group, the frequency of Lactobacillus sp. detected was significantly higher in the dentine surface (p = 0.031) than over the cavitated lesion. The highest frequency of bacteria detected in the intact surfaces was Fusobacterium nucleatum subsp. polymorphum (33.3%) while Streptococcus mutans was detected over the carious lesions and dentine surfaces at a frequency of 33.3% and 52.7% respectively. Fusobacterium nucleatum subsp. polymorphum was also found to be highest in the CF group (41.6%). Follow up at the end of one year showed that the frequency of Corynebacterium matruchotii detected was highest in those who remained caries free (16.6%), while Porphyromonas catoniae was highest in those who developed caries (25%). In conclusion, Streptococcus mutans and Porphyromonas catoniae are strongly associated with caries progression, while Lactobacillus sp. is restricted to deep carious lesions. Fusobacterium nucleatum subsp. polymorphum and Corynebacterium matruchotii may play a role in sustaining the healthy equilibrium in the dental plaque. These identified bacteria show promise as potential biomarkers in diagnosis which could help in the management of dental caries in children.

Keywords: early childhood caries, genotypic identification, oral bacteria, 16S rRNA

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Authors: Ebru Acuner, Gulgun Kayakutlu, M. Ozgur Kayalica, Sermin Onaygil

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In Turkey, emigration, especially from Syria, has been continuously increasing together with rapid urbanization. In parallel to this, total energy consumption has been growing, rapidly. Unfortunately, domestic energy sources could not meet this energy demand. Hence, there is a need for reliable predictions. For this reason, before making a survey study for the migrated people, an informative questionnaire was prepared to take the opinions of the experts on the main drivers that shape the energy consumption behavior of the migrated people. Totally, 17 experts were answered, and they were analyzed by means of Netica program considering Bayesian belief analysis method. In the analysis, factors affecting energy consumption behaviors as well as strategies, institutions, tools and financing methods to change these behaviors towards efficient consumption were investigated. On the basis of the results, it can be concluded that changing the energy consumption behavior of the migrated people is crucial. In order to be successful, electricity and natural gas prices and tariffs in the market should be arranged considering energy efficiency. In addition, support mechanisms by not only the government but also municipalities should be taken into account while preparing related policies. Also, electric appliance producers should develop and implement strategies and action in favor of the usage of more efficient appliances. Last but not least, non-governmental organizations should support the migrated people to improve their awareness on the efficient consumption for the sustainable future.

Keywords: Bayesian belief, behavior, energy consumption, energy efficiency, migrated people

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Authors: Sundus Mona, Atif Adnan, Babar Ali, Fareeha Arshad, Allah Rakha

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Molecular diversity is the variation in the abundance of species. Forensic entomology is a neglected field in Pakistan. Insects collected from the crime scene should be handled by forensic entomologists who are currently virtually non-existent in Pakistan. Correct identification of insect specimen along with knowledge of their biodiversity can aid in solving many problems related to complicated forensic cases. Inadequate morphological identification and insufficient thermal biological studies limit the entomological utility in Forensic Medicine. Recently molecular identification of entomological evidence has gained attention globally. DNA barcoding is the latest and established method for species identification. Only proper identification can provide a precise estimation of postmortem intervals. Arthropods are known to be the first tourists scavenging on decomposing dead matter. The objective of the proposed study was to identify species by molecular techniques and analyze their phylogenetic importance with barcoded necrophagous insect species of early succession on human cadavers. Based upon this identification, the study outcomes will be the utilization of established DNA bar codes to identify carrion feeding insect species for concordant estimation of post mortem interval. A molecular identification method involving sequencing of a 658bp ‘barcode’ fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene from collected specimens of unknown dipteral species from cadavers of Lahore was evaluated. Nucleotide sequence divergences were calculated using MEGA 7 and Arlequin, and a neighbor-joining phylogenetic tree was generated. Three species were identified, Chrysomya megacephala, Chrysomya saffranea, and Chrysomya rufifacies with low genetic diversity. The fixation index was 0.83992 that suggests a need for further studies to identify and classify forensically relevant insects in Pakistan. There is an exigency demand for further research especially when immature forms of arthropods are recovered from the crime scene.

Keywords: molecular diversity, DNA barcoding, species identification, forensically relevant

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Authors: Mohammad Reza Zamani Kouhpanji

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Characterizing the fatigue and fracture properties of nanostructures is one of the most challenging tasks in nanoscience and nanotechnology due to lack of a MEMS/NEMS device for generating uniform cyclic loadings at high frequencies. Here, the dynamic response of a recently proposed MEMS/NEMS device under different inputs signals is completely investigated. This MEMS/NEMS device is designed and modeled based on the electromagnetic force induced between paired parallel wires carrying electrical currents, known as Ampere’s Force Law (AFL). Since this MEMS/NEMS device only uses two paired wires for actuation part and sensing part, it represents highly sensitive and linear response for nanostructures with any stiffness and shapes (single or arrays of nanowires, nanotubes, nanosheets or nanowalls). In addition to studying the maximum gains at different resonance frequencies of the MEMS/NEMS device, its dynamical responses are investigated for different inputs and nanostructure properties to demonstrate the capability, usability, and reliability of the device for wide range of nanostructures. This MEMS/NEMS device can be readily integrated into SEM/TEM instruments to provide real time study of the fatigue and fracture properties of nanostructures as well as their softening or hardening behaviors, and initiation and/or propagation of nanocracks in them.

Keywords: MEMS/NEMS devices, paired wire actuators and sensors, dynamical response, fatigue and fracture characterization, Ampere’s force law

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Authors: Vitalii Yu. Kapitan, Aleksandr V. Perzhu, Konstantin V. Nefedev

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The necessity of studying magnetic multilayer structures is explained by the prospects of their practical application as a technological base for creating new storages medium. Magnetic multilayer films have many unique features that contribute to increasing the density of information recording and the speed of storage devices. Multilayer structures are structures of alternating magnetic and nonmagnetic layers. In frame of the classical Heisenberg model, lattice spin systems with direct short- and long-range exchange interactions were investigated by Monte Carlo methods. The thermodynamic characteristics of multilayer structures, such as the temperature behavior of magnetization, energy, and heat capacity, were investigated. The processes of magnetization reversal of multilayer structures in external magnetic fields were investigated. The developed software is based on the new, promising programming language Rust. Rust is a new experimental programming language developed by Mozilla. The language is positioned as an alternative to C and C++. For the Monte Carlo simulation, the Metropolis algorithm and its parallel implementation using MPI and the Wang-Landau algorithm were used. We are planning to study of magnetic multilayer films with asymmetric Dzyaloshinskii–Moriya (DM) interaction, interfacing effects and skyrmions textures. This work was supported by the state task of the Ministry of Education and Science of the Russia # 3.7383.2017/8.9

Keywords: The Monte Carlo methods, Heisenberg model, multilayer structures, magnetic skyrmion

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Authors: Lohendy Munoz-Vargas, Stephen O. Opiyo, Rose Digianantonio, Michele L. Williams, Asela Wijeratne, Gregory Habing

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Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, to author`s best knowledge, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle.

Keywords: dairy cattle, microbiome, periparturient, Salmonella

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Authors: Isik Cetintav, Cenk Misirli, Yilmaz Can

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This work investigates upsetting of the tri-metallic cylindrical billets both experimentally and analytically with a reduction ratio 30%. Steel, brass, and copper are used for the outer and outmost rings and aluminum for the inner core. Two different models have been designed to show material flow and the cavity took place over the two interfaces during forming after this reduction ratio. Each model has an outmost ring material as steel. Model 1 has an outer ring between the outmost ring and the solid core material as copper and Model 2 has a material as brass. Solid core is aluminum for each model. Billets were upset in press machine by using parallel flat dies. Upsetting load was recorded and compared for models and single billets. To extend the tests and compare with experimental procedure to a wider range of inner core and outer ring geometries, finite element model was performed. ABAQUS software was used for the simulations. The aim is to show how contact between outmost ring, outer ring and the inner core are carried on throughout the upsetting process. Results have shown that, with changing in height, between outmost ring, outer ring and inner core, the Model 1 and Model 2 had very good interaction, and the contact surfaces of models had various interface behaviour. It is also observed that tri-metallic materials have lower weight but better mechanical properties than single materials. This can give an idea for using and producing these new materials for different purposes.

Keywords: tri-metallic, upsetting, copper, brass, steel, aluminum

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Authors: Lai Peng, Cristina Pintucci, Dries Seuntjens, José Carvajal-Arroyo, Siegfried Vlaeminck

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Economic incentives drive the implementation of short-cut nitrogen removal processes such as nitritation/denitritation (Nit/DNit) to manage nitrogen in waste streams devoid of biodegradable organic carbon. However, as any biological nitrogen removal process, the potent greenhouse gas nitrous oxide (N2O) could be emitted from Nit/DNit. Challenges remain in understanding the fundamental mechanisms and development of engineered mitigation strategies for N2O production. To provide answers, this work focuses on manure as a model, the biggest wasted nitrogen mass flow through our economies. A sequencing batch reactor (SBR; 4.5 L) was used treating the centrate (centrifuge supernatant; 2.0 ± 0.11 g N/L of ammonium) from an anaerobic digester processing mainly pig manure, supplemented with a co-substrate. Glycerin was used as external carbon source, a by-product of vegetable oil. Out-selection of nitrite oxidizing bacteria (NOB) was targeted using a combination of low dissolved oxygen (DO) levels (down to 0.5 mg O2/L), high temperature (35ºC) and relatively high free ammonia (FA) (initially 10 mg NH3-N/L). After reaching steady state, the process was able to remove 100% of ammonium with minimum nitrite and nitrate in the effluent, at a reasonably high nitrogen loading rate (0.4 g N/L/d). Substantial N2O emissions (over 15% of the nitrogen loading) were observed at the baseline operational condition, which were even increased under nitrite accumulation and a low organic carbon to nitrogen ratio. Yet, higher DO (~2.2 mg O2/L) lowered aerobic N2O emissions and weakened the dependency of N2O on nitrite concentration, suggesting a shift of N2O production pathway at elevated DO levels. Limiting the greenhouse gas emissions (environmental protection) from such a system could be substantially minimized by increasing the external carbon dosage (a cost factor), but also through the implementation of an intermittent aeration and feeding strategy. Promising steps forward have been presented in this abstract, yet at the conference the insights of ongoing experiments will also be shared.

Keywords: mitigation, nitrous oxide, nitritation/denitritation, pig manure

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Authors: Hande Ünlü, Yu Morishita

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The total area of forest land in Japan accounts for 67% of the national land; however, despite this wealth and hundred years history of silviculture, today Japanese forestry faces socio-economic stagnation in forestry. While the growing gap in the people-forest relationship causes the depopulation of many forest villages, this paper introduces a methodology aiming to develop a place-specific approach in revitalizing this relationship. The paper focuses on a case study from Taiki town in the Hokkaido region to analyze the place's specific socio-economic requirements through interviews and workshops with the local experts, researchers, and stakeholders. Based on the analyzed facts, a master outline of design requirements is developed to produce locally sourced architectural embodiments that aim to act as a unifying element between the forests and the people of Taiki town. In parallel, the proposed methodology aims to generate a cycle of research feed and a researcher retreat, a definition given by Memu Earth Lab to the researchers' stay at Memu in Taiki town for a defined period to analyze local resources, for the continuous improvement of the introduced methodology to revitalize the interaction between people and forest through architecture.

Keywords: architecture, Japanese forestry, local timber, people-forest relationship, research platform

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Authors: Bin Bian, Liang Wang

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A hydraulic spherical motion mechanism (HSMM) is proposed. Unlike traditional systems using serial or parallel mechanisms for multi-DOF rotations, the HSMM is capable of implementing continuous 2-DOF rotational motions in a single joint without the intermediate transmission mechanisms. It has some advantages of compact structure, low inertia and high stiffness. However, as HSMM is a nonlinear and multivariable system, it is very complicate to realize accuracy control. Therefore, an augmented active disturbance rejection controller (ADRC) is proposed in this paper. Compared with the traditional PD control method, three compensation items, i.e., dynamics compensation term, disturbance compensation term and nonlinear error elimination term, are added into the proposed algorithm to improve the control performance. The ADRC algorithm aims at offsetting the effects of external disturbance and realizing accurate control. Euler angles are applied to describe the orientation of rotor. Lagrange equations are utilized to establish the dynamic model of the HSMM. The stability of this algorithm is validated with detailed derivation. Simulation model is formulated in Matlab/Simulink. The results show that the proposed control algorithm has better competence of trajectory tracking in the presence of uncertainties.

Keywords: hydraulic spherical motion mechanism, dynamic model, active disturbance rejection control, trajectory tracking

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Authors: Vanessa De Carvalho, Chad MacPherson, Julien Tremblay, Julie Champagne, Stephanie-Anne Girard

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Background: The interactions between bacteria and fungi in the human vaginal microbiome are fundamental to the concept of health and disease. The means by which the microbiota and mycobiota interact is still poorly understood and further studies are necessary to properly characterize this complex ecosystem. The aim of this study was to select a DNA extraction method capable of recovering high qualities of fungal and bacterial DNA from a single vaginal swab. Methods: 11 female volunteers ( ≥ 20 to < 55 years old) self-collected vaginal swabs in triplicates. Three commercial extraction kits: Masterpure Yeast Purification kit (Epicenter), PureLink™ Microbiome DNA Purification kit (Invitrogen), and Quick-DNA™ Fecal/Soil Microbe Miniprep kit (Zymo) were evaluated on the ability to recover fungal and bacterial DNA simultaneously. The extraction kits were compared on the basis of recovery, yield, purity, and the community richness of bacterial (16S rRNA - V3-V4 region) and fungal (ITS1) microbiota composition by Illumina MiSeq amplicon sequencing. Results: Recovery of bacterial DNA was achieved with all three kits while fungal DNA was only consistently recovered with Masterpure Yeast Purification kit (yield and purity). Overall, all kits displayed similar microbiota profiles for the top 20 OTUs; however, Quick-DNA™ Fecal/Soil Microbe Miniprep kit (Zymo) showed more species richness than the other two kits. Conclusion: In the present study, Masterpure Yeast purification kit proved to be a good candidate for purification of high quality fungal and bacterial DNA simultaneously. These findings have potential benefits that could be applied in future vaginal microbiome research. Whilst the use of a single extraction method would lessen the burden of multiple swab sampling, decrease laboratory workload and off-set costs associated with multiple DNA extractions, thoughtful consideration must be taken when selecting an extraction kit depending on the desired downstream application.

Keywords: bacterial vaginosis, DNA extraction, microbiota, mycobiota, vagina, vulvovaginal candidiasis, women’s health

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Authors: Shpresa Agani, Nysret Agani

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Studies have found that women, during the 1st stage of labour, respectively cervical effacement, experience anxiety. This study aims to measure the degree of anxiety during cervical effacement, using Hopkins Symptom Checklist-25 (HSCL-25) for measuring anxiety symptoms (HSCL-25). A randomized prospective study with 300 women during the 1st stage of labour was conducted where cervical effacement percentage in parallel with the symptoms of anxiety was examined. Anxiety degree levels were examined by HSCL-25. Results showed that 81% were primiparous, while 19% were multiparous. All participants experienced anxiety symptoms, and the degree of anxiety depended on the stage of the birth process. Groups-based modeling according to HSCL- 2 identified three distinct groups of anxiety symptoms: group 1 (low degree, 32 cases or 11%), group 2 (mild degree, 186 cases or 62%), and group 3 (high degree, 82 cases or 27%). Depending on the percentage of cervical effacement, the anxiety degree increased. In a cervical effacement of 0-60-%, 125 cases or 41.6% had symptoms of anxiety, while in a cervical effacement of 60-100%, 174 cases or 58.4% had symptoms of anxiety (Chi-Square X2 (4,N=300)=10.755, p=0.02). This study showed a correlation between cervical effacement and the degree of anxiety. Further, it was found that the majority of participants experienced symptoms of anxiety during the cervical effacement process. The degree of anxiety increased in direct proportion to the degree of the cervical effacement process. The higher the percentage of cervical effacement, the higher the degree of anxiety. A continuing assessment of the psychological well-being of women throughout the birth process.

Keywords: anxiety, cervical effacement, pregnancy, HSCL-25

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Authors: Yousef I. Salamin

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Theoretical investigations, analytical as well as numerical, have shown that electrons can be accelerated to GeV energies by the process of cyclotron auto-resonance acceleration (CARA). In CARA, the particle would be injected along the lines of a uniform magnetic field aligned parallel to the direction of propagation of a plane-wave radiation field. Unfortunately, an accelerator based on CARA would be prohibitively too long and too expensive to build and maintain. However, the process stands a better chance of success near the polar cap of a compact object (such as a neutron star, a black hole or a magnetar) or in an environment created in the wake of a binary neutron-star or blackhole merger. Dynamics of the nuclides ₁H¹, ₂He⁴, ₂₆Fe⁵⁶, and ₂₈Ni⁶², in such astrophysical conditions, have been investigated by single-particle calculations and many-particle simulations. The investigations show that these nuclides can reach ZeV energies (1 ZeV = 10²¹ eV) due to interaction with super-intense radiation of wavelengths = 1 and 10 m and = 50 pm and magnetic fields of strengths at the mega- and giga-tesla levels. Examples employing radiation intensities in the range 10³²-10⁴² W/m² have been used. Employing a two-parameter model for representing the radiation field, CARA is analytically generalized to include any state of polarization, and the basic working equations are derived rigorously and in closed analytic form.

Keywords: compact objects, cosmic-ray acceleration, cyclotron auto-resonance, polarization effects, zevatron

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Authors: Yasser Rammah, Wolf-Christian Mueller

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Nonlinear triad interactions in incompressible three-dimensional magnetohydrodynamic (3D-MHD) turbulence are studied by analyzing data from high-resolution direct numerical simulations of decaying isotropic (5123 grid points) and forced anisotropic (10242 x256 grid points) turbulence. An accurate numerical approach toward analyzing nonlinear turbulent energy transfer function and triad interactions is presented. It involves the direct numerical examination of every wavenumber triad that is associated with the nonlinear terms in the differential equations of MHD in the inertial range of turbulence. The technique allows us to compute the spectral energy transfer and energy fluxes, as well as the spectral locality property of energy transfer function. To this end, the geometrical shape of each underlying wavenumber triad that contributes to the statistical transfer density function is examined to infer the locality of the energy transfer. Results show that the total energy transfer is local via nonlocal triad interactions in decaying macroscopically isotropic MHD turbulence. In anisotropic MHD, turbulence subject to a strong mean magnetic field the nonlinear transfer is generally weaker and exhibits a moderate increase of nonlocality in both perpendicular and parallel directions compared to the isotropic case. These results support the recent mathematical findings, which also claim the locality of nonlinear energy transfer in MHD turbulence.

Keywords: magnetohydrodynamic (MHD) turbulence, transfer density function, locality function, direct numerical simulation (DNS)

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Authors: Rym Sassi, Franck Fayon, Mohend Chaouche, Emmanuel Veron, Valerie Montouillout

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The chemical phenomena occurring during cement hydration are complex and interdependent, and even after almost two centuries of studies, they are still difficult to solve for complex mixtures combining different hydraulic binders. Powder-XRD has been widely used for characterizing the crystalline phases in both anhydrous and hydrated cement, but only limited information is obtained in the case of strongly disordered and amorphous phases. In contrast, local spectroscopies like solid-state NMR can provide a quantitative description of noncrystalline phases. In this work, the structural modifications occurring during hydration of a fast-setting ternary binder based on white Portland cement, white calcium aluminate cement, and calcium sulfate were investigated using advanced solid-state NMR methods. We particularly focused on the early stage of the hydration up to 28 days, working with samples whose hydration was controlled and stopped. ²⁷Al MQ-MAS as well as {¹H}-²⁷Al and {¹H}-²⁹Si Cross- Polarization MAS NMR techniques were combined to distinguish all of the aluminum and silicon species formed during the hydration. The NMR quantification of the different phases was conducted in parallel with the XRD analyses. The consumption of initial products, as well as the precipitation of hydraulic phases (ettringite, monosulfate, strätlingite, CSH, and CASH), were unambiguously quantified. Finally, the drawing of the consumption and formation of phases was correlated with mechanical strength measurements.

Keywords: cement, hydration, hydrates structure, mechanical strength, NMR

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Authors: H. Gokdemir

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All structures are subject to vertical and lateral loads. Under these loads, structures make deformations and deformation values of structural elements mustn't exceed their capacity for structural stability. Especially, lateral loads cause critical deformations because of their random directions and magnitudes. Wind load is one of the lateral loads which can act in any direction and any magnitude. Although wind has nearly no effect on reinforced concrete structures, it must be considered for steel structures, roof systems and slender structures like minarets. Therefore, every structure must be able to resist wind loads acting parallel and perpendicular to any side. One of the effective methods for resisting lateral loads is assembling cross steel elements between columns which are called as wind bracing. These cross elements increases lateral rigidity of a structure and prevent exceeding of deformation capacity of the structural system. So, this means cross elements are also effective in resisting earthquake loads too. In this paper; Effects of wind bracing to earthquake resistance of structures are studied. Structure models (with and without wind bracing) are generated and these models are solved under both earthquake and wind loads with different seismic zone parameters. It is concluded by the calculations that; in low-seismic risk zones, wind bracing can easily resist earthquake loads and no additional reinforcement for earthquake loads is necessary. Similarly; in high-seismic risk zones, earthquake cross elements resist wind loads too.

Keywords: wind bracings, earthquake, steel structures, vertical and lateral loads

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Authors: Sohan Sengupta, Arnab Pramanik, Abhrajyoti Ghosh, Maitree Bhattacharyya

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Newly emerged phyto-pathogens and multi drug resistance have been threating the world for last few decades. Actinomycetes, the most endowed group of microorganisms isolated from unexplored regions of the world may be the ultimate solution to these problems. Thus the aim of this study was to isolate several bioactive actinomycetes strains capable of producing antimicrobial secondary metabolite from Sundarbans, the only mangrove tiger land of the world. Fifty four actinomycetes were isolated and analyzed for antimicrobial activity against fifteen test organisms including three phytopathogens. Nine morphologically distinct and biologically active isolates were subjected to polyphasic identification study. 16s rDNA sequencing indicated eight isolates to reveal maximum similarity to the genus streptomyces, whereas one isolate presented only 93.57% similarity with Streptomyces albogriseolus NRRL B-1305T. Seventy-one carbon sources and twenty-three chemical sources utilization assay revealed their metabolic relatedness. Among these nine isolates three specific strains were found to have notably higher degree of antimicrobial potential effective in a broader range including phyto-pathogenic fungus. PCR base whole genome screen for PKS and NRPS genes, confirmed the occurrence of bio-synthetic gene cluster in some of the isolates for novel antibiotic production. Finally the strain SMS_SU21, which showed antimicrobial activity with MIC value of 0.05 mg ml-1and antioxidant activity with IC50 value of 0.242±0.33 mg ml-1 was detected to be the most potential one. True prospective of this strain was evaluated utilizing GC-MS and the bioactive compound responsible for antimicrobial activity was purified and characterized. Rare bioactive actinomycetes were isolated from unexplored heritage site. Diversity of the biosynthetic gene cluster for antimicrobial compound production has also been evaluated. Antimicrobial compound SU21-C has been identified and purified which is active against a broad range of pathogens.

Keywords: actinomycetes, sundarbans, antimicrobial, pks nrps, phyto-pathogens, GC-MS

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Authors: John Masani Nduko, Joseph Wafula Matofari

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Many spontaneously fermented milk products are produced in Kenya, where they are integral to the human diet and play a central role in enhancing food security and income generation via small-scale enterprises. Fermentation enhances product properties such as taste, aroma, shelf-life, safety, texture, and nutritional value. Some of these products have demonstrated therapeutic and probiotic effects although recent reports have linked some to death, biotoxin infections, and esophageal cancer. These products are mostly processed from poor quality raw materials under unhygienic conditions resulting to inconsistent product quality and limited shelf-lives. Though very popular, research on their processing technologies is low, and none of the products has been produced under controlled conditions using starter cultures. To modernize the processing technologies for these products, our study aims at describing the microbiology and biochemistry of a representative Kenyan spontaneously fermented milk product, Mursik using modern biotechnology (DNA sequencing) and their chemical composition. Moreover, co-creation processes reflecting stakeholders’ experiences on traditional fermented milk production technologies and utilization, ideals and senses of value, which will allow the generation of products based on common ground for rapid progress will be discussed. Knowledge of the value of clean starting raw material will be emphasized, the need for the definition of fermentation parameters highlighted, and standard equipment employment to attain controlled fermentation discussed. This presentation will review the available information regarding traditional fermented milk (Mursik) and highlight our current research work on the application of molecular approaches (metagenomics) for the valorization of Mursik production process through starter culture/ probiotic strains isolation and identification, and quality and safety aspects of the product. The importance of the research and future research areas on the same subject will also be highlighted.

Keywords: lactic acid bacteria, high throughput biotechnology, spontaneous fermentation, Mursik

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Authors: Stephanie Fabris Russo, Daiane Costa Guimarães, Jonas Pedro Fabris, Maria Emilia Camargo, Suzana Leitão Russo, José Augusto Andrade Filho

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Among renewable energy sources, solar energy is the one that has stood out. Solar radiation can be used as a thermal energy source and can also be converted into electricity by means of effects on certain materials, such as thermoelectric and photovoltaic panels. These panels are often used to generate energy in homes, buildings, arenas, etc., and have low pollution emissions. Thus, a technological prospecting was performed to find patents related to the use of photovoltaic plates in urban residences. The patent search was based on ESPACENET, associating the keywords photovoltaic and home, where we found 136 patent documents in the period of 1994-2015 in the fields title and abstract. Note that the years 2009, 2010, 2011, 2012, 2013 and 2014 had the highest number of applicants, with respectively, 11, 13, 23, 29, 15 and 21. Regarding the country that deposited about this technology, it is clear that China leads with 67 patent deposits, followed by Japan with 38 patents applications. It is important to note that most depositors, 50% are companies, 44% are individual inventors and only 6% are universities. On the International Patent classification (IPC) codes, we noted that the most present classification in results was H02J3/38, which represents provisions in parallel to feed a single network by two or more generators, converters or transformers. Among all categories, there is the H session, which means Electricity, with 70% of the patents.

Keywords: photovoltaic, urban residences, technology forecasting, prospecting

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Authors: Nadia Naseem, Farwa Batool, Nasir Mehmood, AbdulHannan Nagi

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Background: The incidence and mortality of breast cancer vary significantly in geographically distinct populations. In Pakistan, breast cancer has shown an increase in incidence in young females and is characterized by more aggressive behavior. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. This study investigated the TP53 mutations in molecular subtypes of both nodes negative and positive breast cancer in young Pakistani patients. Material and Methods: p53, Estrogen Receptor (ER), Progesterone Receptor (PR), Her-2 neu and Ki 67 expressions were analyzed immunohistochemically in a series of 75 node negative (A) and 75 node positive (B) young (aged: 19-40 years) breast cancer patients diagnosed between 2014 to 2017 at two leading hospitals of Punjab, Pakistan. Tumor tissue specimens and peripheral blood samples were examined for TP53 mutations by direct sequencing of the gene (exons 4-9). The relation of TP53 mutations to these markers and clinicopathological data was investigated. Results: Mean age of the patients was 32.4 + 9.1 SD. Invasive breast carcinoma was the most frequent histological variant (A=92%, B=94.6%). Grade 3 carcinoma was the commonest grade (A=72%, B=81.3%). Triple negative cases (ER-, PR-, Her-2) formed most of the molecular subtypes (A=44%, B=50.6%). A total of 17.2% (A: 6.6%, B: 10.6%) patients showed TP53 mutations. Mutations were significantly more frequent in triple negative cases (A: 74.8%, B: 62.2%) compared to HER2-positive patients (P < 0.0001). In the multivariate analysis of the whole patient group, the independent prognosticator were triple negative cases (P=0.021), TP53 overexpression by IHC (P=0.001) and advanced-stage disease (P=0.007). No statistically significant correlation between TP53 mutations and clinicopathological parameters was found (P < 0.05). Conclusions: It is concluded that TP53 mutations are infrequently present in breast carcinoma of young Pakistani population and there was no significant correlation between p53 mutation and early onset disease. Immunohistochemically detected TP53 expression in our resource-constrained to set up can be beneficial in predicting mutations at the younger age in our population.

Keywords: immunohistochemistry (IHC), invasive breast carcinoma (IBC), Pakistan, TP53

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Authors: Chaiwat Tantarangsee

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The purposes of this study are: 1) to study the frequent English writing errors of students registering the course: Reading and Writing English for Academic Purposes II, and 2) to find out the results of writing error correction by using coded indirect corrective feedback and writing error treatments. Samples include 28 2nd year English Major students, Faculty of Education, Suan Sunandha Rajabhat University. Tool for experimental study includes the lesson plan of the course; Reading and Writing English for Academic Purposes II, and tool for data collection includes 4 writing tests of short texts. The research findings disclose that frequent English writing errors found in this course comprise 7 types of grammatical errors, namely Fragment sentence, Subject-verb agreement, Wrong form of verb tense, Singular or plural noun endings, Run-ons sentence, Wrong form of verb pattern and Lack of parallel structure. Moreover, it is found that the results of writing error correction by using coded indirect corrective feedback and error treatment reveal the overall reduction of the frequent English writing errors and the increase of students’ achievement in the writing of short texts with the significance at .05.

Keywords: coded indirect corrective feedback, error correction, error treatment, frequent English writing errors

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Authors: Majed Alobudi

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Edward Said is considered among the most prominent figures in postcolonial theoretical studies and his work has largely influenced critical discussion for many decades. And in the globalized world of today where immigration and dislocation are intense and thoroughly discussed, Said`s views on these issues seem more relevant than ever. This paper will endeavor to bring together Said`s theoretical texts and other writings on immigration and exile in parallel. The aim is to try to find a better understanding of Said`s theories on dislocation and exile theoretically and personally. The combination of these two strands of narrative will eventually shed more light on self location in postcolonial theories and further the understanding of Said's theories and personal life narratives. The paper propose the difficulty dislocation poses in counter colonial narratives such as those written by Said. As an exile, the mission of defining the self and the other becomes obscure when place becomes impossible or prohibited. The clear result becomes a self which proclaims rather than inhabits reality, a treat Said criticized in colonial representation. The self becomes trapped between the worlds of distant reality of dislocation and the estranged world of exile. The outcome would reveal a more weakened attempt at defining the self and countering the postcolonial narrative. The reason for such confusion and contradiction is directly connected to place and dis-location. To summarize, the paper proposes to examine and investigate the implications exile and dislocation have inflected on Said as a prominent postcolonial figure and how that affects his theories and personal life. The outcome, it is argued, would be a vast and lasting effect which such colonial and postcolonial phenomenon have on personal and theoretical narratives written by Said.

Keywords: Edward Said, exile, postcolonialism, dislocation

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Authors: Anyeres N. Atehortua Jimenez, J. David Lambraño, Juan Carlos Muñoz

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Navier-Stokes equations (NSE), which describe the dynamics of a fluid, have an important application on modeling waves used for data inversion techniques as full waveform inversion (FWI). In this work a linearized version of NSE and its variables, neglecting deviatoric terms of stress tensor, is presented. In order to get a theoretical modeling of pressure p(x,t) and wave velocity profile c(x,t), a wave equation of visco-acoustic medium (VAE) is written. A change of variables p(x,t)=q(x,t)h(ρ), is made on the equation for the VAE leading to a well known Klein-Gordon equation (KGE) describing waves propagating in variable density medium (ρ) with dispersive term α^2(x). KGE is reduced to a Poisson equation and solved by proposing a specific function for α^2(x) accounting for the energy dissipation and dispersion. Finally, an integral form solution is derived for p(x,t), c(x,t) and kinematics variables like particle velocity v(x,t), displacement u(x,t) and bulk modulus function k_b(x,t). Further, it is compared this visco-acoustic formulation with another form broadly used in the geophysics; it is argued that this formalism is more general and, given its integral form, it may offer several advantages from the modern parallel computing point of view. Applications to minimize the errors in modeling for FWI applied to oils resources in geophysics are discussed.

Keywords: Navier-Stokes equations, modeling, visco-acoustic, inversion FWI

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Authors: Ali Asghar Sotoudeh

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Mediation Diplomacy has emerged as one of the main pillars of China's foreign policy goals and practices, and Beijing has established itself as a peacekeeping force in regional conflicts and crises such as Afghanistan, Syria, Sudan, Yemen, and the Arab-Israeli peace process. China is deepening and intensifying its diplomatic interventions in the Middle East and trying to shape the security and political developments in the Middle East. On the other hand, economically, China has become one of the most important trading partners with Middle Eastern governments. China is also seeking to expand its foreign policy and economic interests in the Middle East through the New Silk Road initiative and has signed cooperation agreements with 17 Arab countries. In this regard, due to the importance of the subject, this research focuses on answering this question; what is the basis of China's political mediation and economic expansionism in the Middle East? In parallel with this question, this study follows the hypothesis that the mediating role of peace is a legitimate way for China to intervene in Middle East political crises, Without causing China to deviate from its traditional guiding principles based on non-interference in the internal affairs of other actors in the international system. This policy also promotes the security of economic interests and increases the country's political influence in the Middle East. The research method is descriptive-analytical based on the qualitative method, and the data collection method is library and internet resources.

Keywords: China, middle east, political mediation, economic expansionism

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Authors: Kazunari Ozaki, Mitsuru Kageyama, Kenki Miyazawa, Yoshio Nakamura

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Background: Kampo (Japanese Traditional medicine) is a medicine traditionally practiced in Japan, based on ancient Chinese medicine. Most Kampo doctors have used decoction of crude drug pieces for treatment. 93% of the Kampo drugs sold in Japan are Kampo products nowadays. Of all Kampo products, 81% of them are Kampo extract formulations for prescription, which is prepared in powdered or granulated form from medicinal crude drug extracts mixed with appropriate excipient. Physicians with medical license for Western medicine prescribe these Kampo extract formulations for prescription in Japan. Objectives: Our study aims at presenting a brief history of Kampo extract formulations for prescription in Japan. Methods: Systematic searches for relevant studies were conducted using not only printed journals but also electronic journals from the bibliographic databases, such as PubMed/Medline, Ichushi-Web, and university/institutional websites, as well as search engines, such as Google and Google Scholar. Results: The first commercialization of Kampo extract formulations for general use (or OTC (over-the-counter) Kampo extract formulation) was achieved after 1957. The number of drugs has been subsequentially increased, reaching 148 Kampo extract formulation for prescription currently. Conclusion: We provide a history of Kampo extract formulations for prescription in Japan. The originality of this research is that it analyzes the background history of Kampo in parallel with relevant transitions in the government and insurance systems.

Keywords: health insurance system, history, Kampo, Kampo extract formulation for prescription, OTC Kampo extract formulation, pattern corresponding prescription (Ho-sho-so-tai) system

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Authors: Zeina Bourhane, Anders Lanzen, Christine Cagnon, Olfa Ben Said, Cristiana Cravo-Laureau, Robert Duran

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The anthropogenic pressure in coastal areas increases dramatically with the exploitation of environmental resources. Biomonitoring coastal areas are crucial to determine the impact of pollutants on bacterial communities in soils and sediments since they provide important ecosystem services. However, relevant biomonitoring tools allowing fast determination of the ecological status are yet to be defined. Microbial ecology approaches provide useful information for developing such microbial monitoring tools reporting on the effect of environmental stressors. Chemical and microbial molecular approaches were combined in order to determine microbial bioindicators for assessing the ecological status of soil and river ecosystems around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected along soil/river/lake continuums in three stations around the Ichkeul Lake influenced by different human activities at two seasons (summer and winter). Contaminant pressure indexes (PI), including PAHs (Polycyclic aromatic hydrocarbons), alkanes, and OCPs (Organochlorine pesticides) contents, showed significant differences in the contamination level between the stations with seasonal variation. Bacterial communities were characterized by 16S ribosomal RNAs (rRNA) gene metabarcoding. Although microgAMBI indexes, determined from the sequencing data, were in accordance with contaminant contents, they were not sufficient to fully explain the PI. Therefore, further microbial indicators are still to be defined. The comparison of bacterial communities revealed the specific microbial assemblage for soil, river, and lake sediments, which were significantly correlated with contaminant contents and PI. Such observation offers the possibility to define a relevant set of bioindicators for reporting the effects of human activities on the microbial community structure. Such bioindicators might constitute useful monitoring tools for the management of microbial communities in coastal areas.

Keywords: bacterial communities, biomonitoring, contamination, human impacts, microbial bioindicators

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

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

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

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