Search results for: human genome sequencing

Authors: Ruchi Pathania, Ahmad Ahmad, Shireesh Srivastava

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Cyanobacteria is a promising microbe that can capture and convert atmospheric CO₂ and light into valuable industrial bio-products like biofuels, biodegradable plastics, etc. Among their most attractive traits are faster autotrophic growth, whole year cultivation using non-arable land, high photosynthetic activity, much greater biomass and productivity and easy for genetic manipulations. Cyanobacteria store carbon in the form of glycogen which can be hydrolyzed to release glucose and fermented to form bioethanol or other valuable products. Marine cyanobacterial species are especially attractive for countries with scarcity of freshwater. We recently identified a marine native cyanobacterium Synechococcus sp. BDU 130192 which has good growth rate and high level of polyglucans accumulation compared to Synechococcus PCC 7002. In this study, firstly we sequenced the whole genome and the sequences were annotated using the RAST server. Genome scale metabolic model (GSMM) was reconstructed through COBRA toolbox. GSMM is a computational representation of the metabolic reactions and metabolites of the target strain. GSMMs construction through the application of Flux Balance Analysis (FBA), which uses external nutrient uptake rates and estimate steady state intracellular and extracellular reaction fluxes, including maximization of cell growth. The model, which we have named isyn942, includes 942 reactions and 913 metabolites having 831 metabolic, 78 transport and 33 exchange reactions. The phylogenetic tree obtained by BLAST search revealed that the strain was a close relative of Synechococcus PCC 7002. The flux balance analysis (FBA) was applied on the model iSyn942 to predict the theoretical yields (mol product produced/mol CO₂ consumed) for native and non-native products like acetone, butanol, etc. under phototrophic condition by applying metabolic engineering strategies. The reported strain can be a viable strain for biotechnological applications, and the model will be helpful to researchers interested in understanding the metabolism as well as to design metabolic engineering strategies for enhanced production of various bioproducts.

Keywords: cyanobacteria, flux balance analysis, genome scale metabolic model, metabolic engineering

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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: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Elizabeth Starzycka-Korbas, Michal Starzycki, Wojciech Rybinski, Mirosława Dabert

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For a few years, the populations of pathogenic fungi occurring in winter oilseed rape in Malyszyn were analyzed. Brassica napus L. in Poland and in the world is a source of energy for both the men (oil), and animals, as post-extraction middling, as well as a motor fuel (oil, biofuel) therefore studies of this type are very important. The species composition of pathogenic fungi can be an indicator of seed yield. The occurrence of oilseed rape pathogens during several years were analyzed using the sequencing method DNA ITS. The results were compared in the gene bank using the program NCBI / BLAST. In field conditions before harvest of oilseed rape presence of pathogens infesting B. napus has been assessed. For example, in 2015, 150 samples have been isolated and applied to PDA medium for the identification of belonging species. From all population has been selected mycelium of 83 isolates which were sequenced. Others (67 isolates) were pathogenic fungi of the genus Alternaria which are easily to recognize. The population of pathogenic species on oilseed rape have been identified after analyzing the DNA ITS and include: Leptosphaeria sp. 38 (L. maculans 25, L. biglobosa 13), Alternaria sp. 29, Fusarium sp. 3, Sclerotinia sclerotiorum 7, heterogeneous 6, total of 83 isolates. The genus Alternaria sp. fungi wear the largest share of B. napus pathogens in particular years. Another dangerous species for oilseed rape was Leptosphaeria sp. Populations of pathogens in each year were different. The number of pathogens occurring in the field and their composition is very important for breeders and farmers because of the possible selection of the most resistant genotypes for sowing in the next growing season.

Keywords: B. napus, DNA ITS Sequencing, pathogenic fungi, population

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Authors: Rohit Singh Dangi, Ravi Kant Pal, Monica Sundd

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Acyl-CoA binding protein (ACBP) is a housekeeping protein which functions as an intracellular carrier of acyl-CoA esters. Given the fact that the amastigote stage (blood stage) of Leishmania depends largely on fatty acids as the energy source, of which a large part is derived from its host, these proteins might have an important role in its survival. In Leishmania major, genome sequencing suggests the presence of six ACBPs, whose function remains largely unknown. For functional and structural characterization, one of the ACBP genes was cloned, and the protein was expressed and purified heterologously. Acyl-CoA ester binding and stoichiometry were analyzed by isothermal titration calorimetry and Dynamic light scattering. Our results shed light on high affinity of ACBP towards longer acyl-CoA esters, such as myristoyl-CoA to arachidonoyl-CoA with single binding site. To understand the binding mechanism & dynamics, Nuclear magnetic resonance assignments of this protein are being done. The protein's crystal structure was determined at 1.5Å resolution and revealed a classical topology for ACBP, containing four alpha-helical bundles. In the binding pocket, the loop between the first and the second helix (16 – 26AA) is four residues longer from other extensively studied ACBPs (PfACBP) and it curls upwards towards the pantothenate moiety of CoA to provide a large tunnel space for long acyl chain insertion.

Keywords: acyl-coa binding protein (ACBP), acyl-coa esters, crystal structure, isothermal titration, calorimetry, Leishmania

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Authors: Debbarma Asis, Guha Chandan

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Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

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Authors: Shilpi, Indu Gaur, Neha Bhadauria, Susmita Goswami, Prabir K. Paul

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Cultivation and consumption of organically grown fruits and vegetables have increased by several folds. However, the presence of Human Enteric Pathogens on the surface of organically grown vegetables causing Gastro-intestinal diseases, are most likely due to contaminated water and fecal matter of farm animals. Human Enteric Pathogens are adapted to colonize the human gut, and also colonize plant surface. Microbes on plant surface communicate with each other to establish quorum sensing. The cross talk study is important because the enteric pathogens on phylloplane have been reported to mask the beneficial resident bacteria of plant. In the present study, HEPs and bacterial colonizers were identified using 16s rRNA sequencing. Microbial colonization patterns after interaction between Human Enteric Pathogens and natural bacterial residents on tomato phylloplane was studied. Tomato plants raised under aseptic conditions were inoculated with a mixture of Serratia fonticola and Klebsiella pneumoniae. The molecules involved in cross-talk between Human Enteric Pathogens and regular bacterial colonizers were isolated and identified using molecular techniques and HPLC. The colonization pattern was studied by leaf imprint method after 48 hours of incubation. The associated protein-protein interaction in the host cytoplasm was studied by use of crosslinkers. From treated leaves the crosstalk molecules and interaction proteins were separated on 1D SDS-PAGE and analyzed by MALDI-TOF-TOF analysis. The study is critical in understanding the molecular aspects of HEP’s adaption to phylloplane. The study revealed human enteric pathogens aggressively interact among themselves and resident bacteria. HEPs induced establishment of a signaling cascade through protein-protein interaction in the host cytoplasm. The study revealed that the adaptation of Human Enteric Pathogens on phylloplane of Solanum lycopersicum involves the establishment of complex molecular interaction between the microbe and the host including microbe-microbe interaction leading to an establishment of quorum sensing. The outcome will help in minimizing the HEP load on fresh farm produce, thereby curtailing incidences of food-borne diseases.

Keywords: crosslinkers, human enteric pathogens (HEPs), phylloplane, quorum sensing

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Authors: Gunta Resevica, Nikita Zrelovs, Ivars Silamikelis, Ieva Kalnciema, Helvijs Niedra, Gunārs Lācis, Toms Bartulsons, Inga Moročko-Bičevska, Arturs Stalažs, Kristīne Drevinska, Andris Zeltins, Ina Balke

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Newly discovered viruses provide novel knowledge for basic phytovirus research, serve as tools for biotechnology and can be helpful in identification of epidemic outbreaks. Blackcurrant-associated rhabdovirus (BCaRV) have been discovered in USA germplasm collection samples from Russia and France. As it was reported in one accession originating from France it is unclear whether the material was already infected when it entered in the USA or it became infected while in collection in the USA. Due to that BCaRV was definite as non-EU viruses. According to ICTV classification BCaRV is representative of Blackcurrant betanucleorhabdovirus specie in genus Betanucleorhabdovirus (family Rhabdoviridae). Nevertheless, BCaRV impact on the host, transmission mechanisms and vectors are still unknown. In RNA-seq data pool from Ribes plants resistance gene study by high throughput sequencing (HTS) we observed differences between sample group gene transcript heat maps. Additional analysis of the whole data pool (total 393660492 of 150 bp long read pairs) by rnaSPAdes v 3.13.1 resulted into 14424 bases long contig with an average coverage of 684x with shared 99.5% identity to the previously reported first complete genome of BCaRV (MF543022.1) using EMBOSS Needle. This finding proved BCaRV presence in EU and indicated that it might be relevant pathogen. In this study leaf tissue from twelve asymptomatic blackcurrant cv. Mara Eglite plants (negatively tested for blackcurrant reversion virus (BRV)) from Dobele, Latvia (56°36'31.9"N, 23°18'13.6"E) was collected and used for total RNA isolation with RNeasy Plant Mini Kit with minor modifications, followed by plant rRNA removal by a RiboMinus Plant Kit for RNA-Seq. HTS libraries were prepared using MGI Easy RNA Directional Library Prep Set for 16 reactions to obtain 150 bp pair-end reads. Libraries were pooled, circularized and cleaned and sequenced on DNBSEQ-G400 using PE150 flow cell. Additionally, all samples were tested by RT-PCR, and amplicons were directly sequenced by Sanger-based method. The contig representing the genome of BCaRV isolate Mara Eglite was deposited at European Nucleotide Archive under accession number OU015520. Those findings indicate a second evidence on the presence of this particular virus in the EU and further research on BCaRV prevalence in Ribes from other geographical areas should be performed. As there are no information on BCaRV impact on the host this should be investigated, regarding the fact that mixed infections with BRV and nucleorhabdoviruses are reported.

Keywords: BCaRV, Betanucleorhabdovirus, Ribes, RNA-seq

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Authors: Abanoub Zare Zakaria Herzalla

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The link between terrorism and human rights has become a major challenge in the fight against terrorism around the world. This is based on the fact that terrorism and human rights are so closely linked that when the former starts, the latter are violated. This direct connection was recognized in the Vienna Declaration and Program of Action adopted by the World Conference on Human Rights in Vienna on June 25, 1993, which recognizes that acts of terrorism in all their forms and manifestations aim to destroy the human rights of people. Terrorism therefore represents an attack on our most basic human rights. To this end, the first part of this article focuses on the connections between terrorism and human rights and seeks to highlight the interdependence between these two concepts. The second part discusses the emerging concept of cyberterrorism and its manifestations. An analysis of the fight against cyberterrorism in the context of human rights is also carried out.

Keywords: sustainable development, human rights, the right to development, the human rights-based approach to development, environmental rights, economic development, social sustainability human rights protection, human rights violations, workers’ rights, justice, security.

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Authors: Tarek Aboueldahab, Hanan Farag

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Parallel Job Shop Scheduling Problem (JSP) is a multi-objective and multi constrains NP- optimization problem. Traditional Artificial Intelligence techniques have been widely used; however, they could be trapped into the local minimum without reaching the optimum solution, so we propose a hybrid Artificial Intelligence model (AI) with Discrete Breeding Swarm (DBS) added to traditional Artificial Intelligence to avoid this trapping. This model is applied in the cost minimization of the Car Sequencing and Operator Allocation (CSOA) problem. The practical experiment shows that our model outperforms other techniques in cost minimization.

Keywords: parallel job shop scheduling problem, artificial intelligence, discrete breeding swarm, car sequencing and operator allocation, cost minimization

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Authors: Joseph Marzouk Gerais Abdelmalak

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The interface between development and human rights has long been the subject of academic debate. Therefore, to understand the dynamics between the two concepts, a number of principles have been adopted, ranging from the right to development to a human rights-based approach to development. Despite these attempts, the exact connection between development and human rights is not yet fully understood. However, the inherent interdependence between these two concepts and the idea that development efforts should be undertaken with respect for human rights guarantees have gained momentum in recent years. It will then be examined whether the right to sustainable development is recognized.The article therefore concludes that the principles of sustainable development are recognized, directly or indirectly, in various human rights instruments, which represents a positive answer to the question posed above. Therefore, this work discusses international and regional human rights instruments as well as case law and interpretative guidelines from human rights bodies to demonstrate this hypothesis.

Keywords: sustainable development, human rights, the right to development, the human rights-based approach to development, environmental rights, economic development, social sustainability human rights protection, human rights violations, workers’ rights, justice, security

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Authors: Mindaugas Kazlauskas

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In this paper, it is presupposed that the description of the relationship between animal and human should begin with a description of the direct experience of the animal and how, in this experience, the human experiences itself (a self awareness mode). A human is concerned first and foremost with himself as a human through the experience of another as an animal. The questionsare: In the encounter with an animal, how is the animal constituted in the acts of human experience? How does human-animal interaction influence human behavioral patterns, and how does the human identifies itself in this interaction? The paper will present the results of interpretative phenomenological descriptions (IPA) of the relationship between human and animal in the face of death phenomenon through the experience of pet owners who lost their beloved companions and hunters, veterinatians, and farmers who face animal death. The results of IPA analysis reveal different relations such as the identification with an animal, the alienation experience, the experience of resistance, and an experience of detachment. Within these themes, IPA qualitative research results will be presented by highlighting patterns of human behavior, following Friedrich Schlachermacher's hermeneutics methodological principles, and reflecting on changes in value and attitude within society during daily interaction with the animal.

Keywords: animal human interaction, phenomenology, philosophy, death phenomenon

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Authors: Shenouda Farag Aziz Ibrahim

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The relationship between terrorism and human rights has become an important issue in the fight against terrorism worldwide. This is based on the fact that terrorism and human rights are closely linked, so that when the former begins, the latter suffers. This direct link was recognized in the Vienna Declaration and Program of Action adopted by the International Conference on Human Rights held in Vienna on 25 June 1993, which recognized that terrorist acts aim to violate human rights in all their forms and manifestations. . Therefore, terrorism represents an attack on fundamental human rights. For this purpose, the first part of this article focuses on the relationship between terrorism and human rights and aims to show the relationship between these two concepts. In the second part, the concept of cyber threat and its manifestations are discussed. An analysis of the fight against terrorism in the context of human rights was also made..

Keywords: sustainable development, human rights, the right to development, the human rights-based approach to development, environmental rights, economic development, social sustainability human rights protection, human rights violations, workers’ rights, justice, security.

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Authors: Ellie Fini, Mahour Parast, Daniel Oldham, Shahrzad Hosseinnezhad

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This paper investigates the relationship between molecular species of four different bio-based adhesives (made from Swine Manure, Miscanthus Pellet, Corn Stover, and Wood Pellet) and their rheological behavior before and after they undergo extensive oxidative aging. To study the effect of oxidative aging on the chemical structure of bio-adhesives, Infrared Attenuated Total Reflectance Spectroscopy (Fourier transform infrared) was utilised. In addition, a Drop Shape Analyser, Rotational Viscometer, and Dynamic Shear Rheometer were used to evaluate the surface properties and rheological behaviour of each bio-adhesive. Overall, bio-adhesives were found to be significantly different in terms of their ageing characteristics. Accordingly, their surface and rheological properties were found to be ranked differently before and after ageing. The results showed that the bio-adhesive from swine manure is less susceptible to aging compared to plant-based bio-oils. This can be further attributed to the chemical structure and the high lipid contents of the bio-adhesive from swine manure, making it less affected by oxidative ageing.

Keywords: bio-adhesive, rheology, bio-mass, material genome

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Authors: Daniel Osorio, Janneth Gonzalez, Andres Pinzon

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In this work, proteins and metabolic pathways associated with the neuroprotective response mediated by the synthetic neurosteroid tibolone under a palmitate-induced inflammatory model were identified by flux balance analysis (FBA). Three different metabolic scenarios (‘healthy’, ‘inflamed’ and ‘medicated’) were modeled over a gene expression data-driven constructed tissue-specific metabolic reconstruction of mature astrocytes. Astrocyte reconstruction was built, validated and constrained using three open source software packages (‘minval’, ‘g2f’ and ‘exp2flux’) released through the Comprehensive R Archive Network repositories during the development of this work. From our analysis, we predict that tibolone executes their neuroprotective effects through a reduction of neurotoxicity mediated by L-glutamate in astrocytes, inducing the activation several metabolic pathways with neuroprotective actions associated such as taurine metabolism, gluconeogenesis, calcium and the Peroxisome Proliferator Activated Receptor signaling pathways. Also, we found a tibolone associated increase in growth rate probably in concordance with previously reported side effects of steroid compounds in other human cell types.

Keywords: astrocytes, flux balance analysis, genome scale metabolic reconstruction, inflammation, neuroprotection, tibolone

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Authors: Manotar Tampubolon

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Although the Indonesian human rights protection has increased in recent years, but human rights violations still occur in the industrial sector. Crimes against human rights continue to occur and go unnoticed in spite of the government's legislation on human rights, employment law in addition to an international treaty that has been ratified by Indonesia. The increasing number of garment companies in Bekasi, also give rise to increased human rights violations since the government does not have a commitment to protect it. The Indonesian government and industry owners should pay attention to and protect the human rights of workers and treat them accordingly. This paper will review the human rights violations experienced by workers at garment factories in the context of the law, as well as ideas to improve the protection of workers' rights.

Keywords: human rights protection, human rights violations, workers’ rights, justice, security

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Authors: Ali Alattabi, Clare Harris, Rafid Alkhaddar, Ali Alzeyadi

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Petroleum refinery wastewater (PRW) can be considered as one of the most significant source of aquatic environmental pollution. It consists of oil and grease along with many other toxic organic pollutants. In recent years, a new technique was implemented using different types of membranes and sequencing batch reactors (SBRs) to treat PRW. SBR is a fill and draw type sludge system which operates in time instead of space. Many researchers have optimised SBRs’ operating conditions to obtain maximum removal of undesired wastewater pollutants. It has gained more importance mainly because of its essential flexibility in cycle time. It can handle shock loads, requires less area for operation and easy to operate. However, bulking sludge or discharging floating or settled sludge during the draw or decant phase with some SBR configurations are still one of the problems of SBR system. The main aim of this study is to develop and innovative design for the SBR optimising the process variables to result is a more robust and efficient process. Several experimental tests will be developed to determine the removal percentages of chemical oxygen demand (COD), Phenol and nitrogen compounds from synthetic PRW. Furthermore, the dissolved oxygen (DO), pH and oxidation-reduction potential (ORP) of the SBR system will be monitored online to ensure a good environment for the microorganisms to biodegrade the organic matter effectively.

Keywords: petroleum refinery wastewater, sequencing batch reactor, hydraulic retention time, Phenol, COD, mixed liquor suspended solids (MLSS)

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Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

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Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Perihan Hazel Kaya, Mustafa Göktuğ Kaya

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Turkey has been a busy destination for immigration and it will always be as it is the geographical and cultural exit door of the East and the entrance door of the West. Among these immigrations, we can see the victims of human trafficking, human smuggling, refugees and those who came here to work and live. Human smuggling, which is one of the movements of illegal immigration, is the specific subject of this work. The fact that our country lies on the transportation destinations between the continents of Asia, Europe and Africa, the crime of human smuggling is highly committed in our country. The aim of the victims of human smuggling is to go to a more developed country to have higher standards of living, to get a better job and to escape from the economic and social instability of their countries. The human smuggling, which has gathered pace due to the improvements in communication and transportation, is not a regional issue and has become one of the most important problems for almost all countries. Accordingly, the reasons, methods and extent of human smuggling will be dealt firstly. Later, it will be studied why Turkey is preffered in human smuggling. Finally, statistical data will be given to show how much human smuggling has gone far in Turkey and the study will be finished with that what is being done and what can be done to prevent it.

Keywords: human smuggling, immigration, immigrator, human trafficking, Turkey

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Authors: Mohammed Ali

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In this paper, evaluation of flexible manufacturing system is made under different manufacturing strategies. The objective of this paper is to test the impact of pallets and routing flexibility on system performance operating at different sequencing rules, dispatching rules and at unbalanced load condition. A computer simulation model is developed to evaluate the effects of aforementioned manufacturing strategies on the make-span performance of flexible manufacturing system. The impact of number of pallets is shown with the different levels of routing flexibility. In this paper, the same manufacturing system is modeled under different combination of sequencing and dispatching rules. A series of simulation experiments are conducted and results analyzed. The result of the simulation shows that there is impact of pallets and routing flexibility on the performance of the system.

Keywords: flexibility, flexible manufacturing system, pallets, make-span, simulation

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Authors: Huajuan Shi

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Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: Seung-Un Chae, Heung-Yul Kim, Sa-Kil Kim

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This paper presents the findings of preliminary study on human control performance in case of fire. The relationship between human control and human decision is studied in decision processes and stress model of human in a fire. Human behavior aspects involved in the decision process during a fire incident. The decision processes appear that six of individual perceptual processes: recognition, validation, definition, evaluation, commitment, and reassessment. Then, human may be stressed in order to get an optimal decision for their activity. This paper explores problems in human control processes and stresses in a catastrophic situation. Thus, the future approach will be concerned to reduce stresses and ambiguous irrelevant information.

Keywords: human reliability, decision processes, stress model, fire

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Authors: Arenca Trashani

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20 years after its first entrance in a General Assembly of the United Nation’s Resolution, human security has became a very important tool in a global debate affecting directly the whole main rules and regulations in international law and more closely in international human rights law. This paper will cover a very important issue of today at how the human security has its impact to the development of international human rights law, not as far as a challenge as it is seen up now but a tool of moving toward development and globalization. In order to analyze the impact of human security to the global agenda, we need to look to the main pillars of the international legal order which are affected by the human security in itself and its application in the policy making for this international legal order global and regional ones. This paper will focus, also, on human security, as a new and very important tool of measuring development, stability and the level of democratic consolidation and the respect for human rights especially in developing countries such as Albania. The states are no longer capable to monopolize the use of human security just within their boundaries and separated from the other principles of a functioning democracy. In this context, human security would be best guaranteed under the respect of the rule of law and democratization. During the last two decades the concept security has broadly developed, from a state-centric to a more human-centric approach: from state security to respect for human rights, to economic security, to environmental security as well. Last but not least we would see that human rights could be affected by human security not just at their promotion but also at their enforcement and mainly at the international institutions, which are entitled to promote and to protect human rights.

Keywords: human security, international human rights law, development, Albania, international law

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Authors: Swarkar Sharma, Ekta Rai, Ankit Mahajan, Parvinder Kumar, Manoj K Dhar, Sushil Razdan, Kumarasamy Thangaraj, Carol Wise, Shiro Ikegawa M.D., K.K. Pandita M.D.

Abstract:

Rare disorders are poorly understood hence, remain uncharacterized or patients are misdiagnosed and get poor medical attention. A rare mysterious skeletal disorder that remained unidentified for decades and rendered many people physically challenged and disabled for life has been reported in an isolated remote village ‘Arai’ of Poonch district of Jammu and Kashmir. This village is located deep in mountains and the population residing in the region is highly consanguineous. In our survey of the region, 70 affected people were reported, showing similar phenotype, in the village with a population of approximately 5000 individuals. We were able to collect samples from two multi generational extended families from the village. Through Whole Exome sequencing (WES), we identified a rare variation NM_003880.3:c.156C>A NP_003871.1:p.Cys52Ter, which results in introduction of premature stop codon in WISP3 gene. We found this variation perfectly segregating with the disease in one of the family. However, this variation was absent in other family. Interestingly, a novel splice site mutation at position c.643+1G>A of WISP3 gene, perfectly segregating with the disease was observed in the second family. Thus, exploiting WES and putting different evidences together (familial histories and genetic data, clinical features, radiological and biochemical tests and findings), the disease has finally been diagnosed as a very rare recessive hereditary skeletal disease “Progressive Pseudorheumatoid Arthropathy of Childhood” (PPAC) also known as “Spondyloepiphyseal Dysplasia Tarda with Progressive Arthropathy” (SEDT-PA). This genetic characterization and identification of the disease causing mutations will aid in genetic counseling, critically required to curb this rare disorder and to prevent its appearance in future generations in the population. Further, understanding of the role of WISP3 gene the biological pathways should help in developing treatment for the disorder.

Keywords: whole exome sequencing, Next Generation Sequencing, rare disorders

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Authors: Ayman K. El Essawy, Amal M. Hosny, Hala M. Abu Shady

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The rapid detection of TB and drug resistance, both optimizes treatment and improves outcomes. In the current study, respiratory specimens were collected from 155 patients. Conventional susceptibility testing and MIC determination were performed for rifampicin (RIF) and isoniazid (INH). Genotype MTBDRplus assay, which is a molecular genetic assay based on the DNA-STRIP technology and specific gene sequencing with primers for rpoB, KatG, and mab-inhA genes were used to detect mutations associated with resistance to rifampicin and isoniazid. In comparison to other categories, most of rifampicin resistant (61.5%) and isoniazid resistant isolates (47.1%) were from patients relapsed in treatment. The genotypic profile (using Genotype MTBDRplus assay) of multi-drug resistant (MDR) isolates showed missing of katG wild type 1 (WT1) band and appearance of mutation band katG MUT2. For isoniazid mono-resistant isolates, 80% showed katG MUT1, 20% showed katG MUT1, and inhA MUT1, 20% showed only inhA MUT1. Accordingly, 100% of isoniazid resistant strains were detected by this assay. Out of 17 resistant strains, 16 had mutation bands for katG distinguished high resistance to isoniazid. The assay could clearly detect rifampicin resistance among 66.7% of MDR isolates that showed mutation band rpoB MUT3 while 33.3% of them were considered as unknown. One mono-resistant rifampicin isolate did not show rifampicin mutation bands by Genotype MTBDRplus assay, but it showed an unexpected mutation in Codon 531 of rpoB by DNA sequence analysis. Rifampicin resistance in this strain could be associated with a mutation in codon 531 of rpoB (based on molecular sequencing), and Genotype MTBDRplus assay could not detect the associated mutation. If the results of Genotype MTBDRplus assay and sequencing were combined, this strain shows hetero-resistance pattern. Gene sequencing of eight selected isolates, previously tested by Genotype MTBDRplus assay, could detect resistance mutations mainly in codon 315 (katG gene), position -15 in inhA promotes gene for isoniazid resistance and codon 531 (rpoB gene) for rifampicin resistance. Genotyping techniques allow distinguishing between recurrent cases of reinfection or reactivation and supports epidemiological studies.

Keywords: M. tuberculosis, rpoB, KatG, inhA, genotype MTBDRplus

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Authors: Allan Munyao Mukuki

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The nexus between terrorism and human rights has become a big challenge in the fight against terrorism globally. This is hinged on the fact that terrorism and human rights are interrelated to the extent that, when the former starts, the latter is violated. This direct linkage was recognised in the Vienna Declaration and Programme of Action as adopted by the World Conference on Human Rights in Vienna on 25 June 1993 which agreed that acts of terrorism in all its forms and manifestations are aimed at the destruction of human rights. Hence, terrorism constitutes an assault on our most basic human rights. To this end, the first part of this paper will focus on the nexus between terrorism and human rights and endeavors to draw a co-relation between these two concepts. The second part thereafter will analyse the emerging concept of cyber-terrorism and how it takes place. Further, an analysis of cyber counter-terrorism balanced as against human rights will also be undertaken. This will be done through the analysis of the concept of ‘securitisation’ of human rights as well as the need to create a balance between counterterrorism efforts as against the protection of human rights at all costs. The paper will then concludes with recommendations on how to balance counter-terrorism and human rights in the modern age.

Keywords: balance, counter-terrorism, cyber-terrorism, human rights, security, violation

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Authors: Ayyoub Jamali

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At the first glance, it seems that the African Court on Human and People’s Rights has achieved a tremendous development in the protection of human rights in Africa. Since its first judgement in 2009, the court has taken a robust approach/ assertive stance, showing its strength by finding states to be in violation of the Africana Charter and other human rights treaties. This paper seeks to discuss various challenges and resistance that the Court has faced since the adoption of the Founding Protocol to the Establishment of the African Court on Human and People’s Rights. The outcome of the paper casts shadow on the legitimacy and effectiveness of the African Court as the guarantor of human rights within the African continent.

Keywords: African Court on Human and People’s Rights, African Union, African regional human rights system, compliance

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Authors: Lata Kumari Dhanesh Tiwary, Pradeep Kumar Mishra

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The effluent coming from various industries such as textile, carpet, food, pharmaceutical and many other industries is big challenge due to its recalcitrant and xenobiotiocs in nature. Recently, biodegradation of dye wastewater through biological means was widely used due to eco-friendly and cost effective with the higher percentage of removal of dye from wastewater. The present study deals with the biodegradation and decolourization of Direct Red 23 dye using indigenously isolated bacterial consortium. The bacterial consortium was isolated from soil sample from dye contaminated site near a cluster of Carpet industries of Bhadohi, Uttar Pradesh, India. The bacterial strain formed consortia were identified and characterized by morphological, biochemical and 16S rRNA gene sequence analysis. The bacterial strain mainly Staphylococcus saprophyticus strain BHUSS X3 (KJ439576), Microbacterium sp. BHUMSp X4 (KJ740222) and Staphylococcus saprophyticus strain BHUSS X5 (KJ439576) were used as consortia for further studies of dye decolorization. Experimental investigations were made in a Sequencing Air- lift bioreactor using the synthetic solution of Direct Red 23 dye by optimizing various parameters for efficient degradation of dye. The effect of several operating parameters such as flow rate, pH, temperature, initial dye concentration and inoculums size on removal of dye was investigated. The efficiency of isolated bacterial consortia from dye contaminated area in Sequencing Air- lift Bioreactor with different concentration of dye between 100-1200 mg/l at different hydraulic rate (HRTs) 26h and 10h. The maximum percentage of dye decolourization 98% was achieved when operated at HRT of 26h. The percentage of decolourization of dye was confirmed by using UV-Vis spectrophotometer and HPLC.

Keywords: carpet industry, bacterial consortia, sequencing air-lift bioreactor

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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