Search results for: plant genome organisation

Authors: N. P. Eswara Reddy, S. Thahir Basha

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Here, we report the success stories of potential leaf, seed and root endophytes against soil borne as well as foliar plant pathogens which are nutritionally adequate and safe for consumption. Endophytes are the microorganisms that reside asymptomatically in the tissues of higher plants are a robust source of potential biocontrol agents and it is presumed that the survival ability of endophytes may be better when compared to phylloplane microflora. Of all the 68 putative leaf endophytes, the endophytes viz., EB9 (100%), and EB35 (100%) which were superior in controlling Colletotrichum gloeosporioides causing mango anthracnose were identified as Brevundimonas bullata (EB09) and Bacillus thuringiensis (EB35) and further delayed in ripening of mango fruits up to 21 days. As a part, the seed endophyte GSE-4 was identified as Archoromobacter spp. against Sclerotium rolfsii causing stem rot of groundnut and the root endophyte REB-8 against Rhizoctonia bataticola causing dry root rot of chickpea was identified as Bacillus subtilis. Both recorded least percent disease incidence (PDI) and increased plant growth promotion, respectively. Further, the novel Bacillus subtilis (SEB-2) against Macrophomina pahseolina causing charcoal rot of sunflower provides an ample scope for exploring the endophytes at large scale. The talc-based formulations of these endophytes developed can be commercialized after toxicological studies. At the bottom line these unexplored endophytes are the need of the hour against aggressive plant pathogens and to maintain the quality and abundance of food and feed and also to fetch marginal economy to the farmers will be discussed.

Keywords: endophytes, plant pathogens, commercialization, abundance of food

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: U. Schmidt, D. Dannehl, I. Schuch, J. Suhl, T. Rocksch, R. Salazar-Moreno, E. Fitz-Rodrigues, A. Rojano Aquilar, I. Lopez Cruz, G. Navas Gomez, R. A. Abraham, L. C. Irineo, N. G. Gilberto

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The integration of agricultural production systems into urban areas is a challenge for the coming decades. Because of increasing greenhouse gas emission and rising resource consumption as well as costs in animal husbandry, the dietary habits of people in the 21st century have to focus on herbal foods. Intensive plant cultivation systems in large cities and megacities require a smart coupling of information, material and energy flow with the urban infrastructure in terms of Horticulture 4.0. In recent years, many puzzle pieces have been developed for these closed processes at the Humboldt University. To compile these for an urban plant production, it has to be optimized and networked with urban infrastructure systems. In the field of heat energy production, it was shown that with closed greenhouse technology and patented heat exchange and storage technology energy can be provided for heating and domestic hot water supply in the city. Closed water circuits can be drastically reducing the water requirements of plant production in urban areas. Ion sensitive sensors and new disinfection methods can help keep circulating nutrient solutions in the system for a longer time in urban plant production greenhouses.

Keywords: semi closed, greenhouses, urban farming, solar heat collector, closed water cycles, aquaponics

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Authors: Sadhana Shukla, Pushplata Singh, Nidhi Didwania

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Arbuscular mycorrhizal (AM) fungi are a highly advantageous and versatile group of fungi that significantly contribute to the formation of soil organic matter by creating a demand for plant carbon (C) and distributing it through below-ground hyphal biomass, regardless of their substantial contribution in enhancing net primary productivity and accumulating additional photosynthetic fixed C in the soil. The genetic role of AM fungi in carbon cycling is largely unexplored. In our study, we propose that AM fungi significantly interact with the soil, particularly: the provision of photosynthates by plants. We have studied the expression of AM fungi genes involved in CO₂ sequestration during host-plant interaction was investigated by qPCR studies. We selected Rhizophagus proliferus (AM fungi) and Oryza sativa (Rice) (inoculated with or without 200ppg AMF inoculums per plant) and investigated the effect of AM fungi on soil organic carbon (SOC) and rice growth under field conditions. Results thus provided faster SOC turnover, 35% increased nutrient uptake in plants and pronounced hyphal biomass of AM fungi which enhanced soil carbon storage by 15% in comparison to uninoculated plants. This study will offer a foundation for delving into various carbon-soil studies while also advancing our comprehension of the relationship between AM fungi and the sustainability of agricultural ecosystems.

Keywords: arbuscular mycorrhizal (AM) fungi, carbon sequestration, gene expression, soil health, plant development.

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Authors: Miriam Sosa-Díaz, Faustino Sánchez-Garduño

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In population dynamics the study of both, the abundance and the spatial distribution of the populations in a given habitat, is a fundamental issue a From ecological point of view, the determination of the factors influencing such changes involves important problems. In this paper a mathematical model to describe the temporal dynamic and the spatiotemporal dynamic of the interaction of three populations (pollinators, plants and herbivores) is presented. The study we present is carried out by stages: 1. The temporal dynamics and 2. The spatio-temporal dynamics. In turn, each of these stages is developed by considering three cases which correspond to the dynamics of each type of interaction. For instance, for stage 1, we consider three ODE nonlinear systems describing the pollinator-plant, plant-herbivore and plant-pollinator-herbivore, interactions, respectively. In each of these systems different types of dynamical behaviors are reported. Namely, transcritical and pitchfork bifurcations, existence of a limit cycle, existence of a heteroclinic orbit, etc. For the spatiotemporal dynamics of the two mathematical models a novel factor are introduced. This consists in considering that both, the pollinators and the herbivores, move towards those places of the habitat where the plant population density is high. In mathematical terms, this means that the diffusive part of the pollinators and herbivores equations depend on the plant population density. The analysis of this part is presented by considering pairs of populations, i. e., the pollinator-plant and plant-herbivore interactions and at the end the two mathematical model is presented, these models consist of two coupled nonlinear partial differential equations of reaction-diffusion type. These are defined on a rectangular domain with the homogeneous Neumann boundary conditions. We focused in the role played by the density dependent diffusion term into the coexistence of the populations. For both, the temporal and spatio-temporal dynamics, a several of numerical simulations are included.

Keywords: bifurcation, heteroclinic orbits, steady state, traveling wave

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Authors: Eleonora Di Mario

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This paper describes the application of ground improvement to replace a typical piled foundation scheme in a power plant in Singapore. Several buildings within the plant were founded on vibro-compacted sand, including a turbine unit which had extremely stringent requirements on the allowable settlement. The achieved savings in terms of cost and schedule are presented. The monitoring data collected during the operation of the turbine are compared to the design predictions to validate the design approach, and the quality of the ground improvement works. In addition, the calculated carbon footprint of the ground improvement works are compared to the piled solution, showing that the vibro-compaction has a significantly lower carbon footprint.

Keywords: ground improvement, vibro-compaction, case study, sustainability, carbon footprint

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Authors: Umar Jaafar, Mungadi

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Plant growth, biochemical parameters, cytotoxic ion sequestration and ionic in balance were determined for spinach in response to varied concentrations of NaCl. The plant show decline in all vegetative parameters measured. Free proline content increase with increasing salt concentration and differ significantly (p<0.05) while the glycine betaine insignificantly (p>0.05) affected by concentration of NaCl. Salinity increases the cytotoxic ions, sodium chlorine ion and calcium with corresponding decrease in potassium ion concentrations. The ionic balance (Na+/K+) is low due to high content of potassium ion in plant accumulation ranging from 7700 to 6500 mg/kg. It can be concluded that the osmolyte accumulations, high number of leaves are possible indicators of salt tolerance in the spinach.

Keywords: spinach, salinity, osmolyte, cytotoxic

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Authors: Ahmeda Ali, Mary Codd, Susan Brundage

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Importance: This research focuses on devising and improving Health Service Executive (HSE) policy and legislation and therefore improving patient trauma care and outcomes in Ireland. Objectives: The study measures components of the Trauma System in the district hospital setting of the Cavan/Monaghan Hospital Group (CMHG), HSE, Ireland, and uses the collected data to identify the strengths and weaknesses of the CMHG Trauma System organisation, to include governance, injury data, prevention and quality improvement, scene care and facility-based care, and rehabilitation. The information will be made available to local policy makers to provide objective situational analysis to assist in future trauma service planning and service provision. Design, setting and participants: From 28 April to May 28, 2016 a cross-sectional survey using World Health Organisation (WHO) Trauma System Assessment Tool (TSAT) was conducted among healthcare professionals directly involved in the level III trauma system of CMHG. Main outcomes: Identification of the strengths and weaknesses of the Trauma System of CMHG. Results: The participants who reported inadequate funding for pre hospital (62.3%) and facility based trauma care at CMHG (52.5%) were high. Thirty four (55.7%) respondents reported that a national trauma registry (TARN) exists but electronic health records are still not used in trauma care. Twenty one respondents (34.4%) reported that there are system wide protocols for determining patient destination and adequate, comprehensive legislation governing the use of ambulances was enforced, however, there is a lack of a reliable advisory service. Over 40% of the respondents reported uncertainty of the injury prevention programmes available in Ireland; as well as the allocated government funding for injury and violence prevention. Conclusions: The results of this study contributed to a comprehensive assessment of the trauma system organisation. The major findings of the study identified three fundamental areas: the inadequate funding at CMHG, the QI techniques and corrective strategies used, and the unfamiliarity of existing prevention strategies. The findings direct the need for further research to guide future development of the trauma system at CMHG (and in Ireland as a whole) in order to maximise best practice and to improve functional and life outcomes.

Keywords: trauma, education, management, system

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Authors: Muhammad Rafiq Shahid, Ali Hassan, Umm-e- Rubab, Muhammad Nadeem

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Insecticidal property of plant extracts was assessed toward dusky bug of cotton. Plant extracts consisted of bari pata (Ziziphus jajuba), Ak (Calotropis gigantean), Tobacco (Nicotiana tabacum), Bakine (Melia azedarach),Kanar (Nerium oleander),Kurtuma (Mitragyna speciosa) and one Control was also included with distilled water treatment. Forced feeding experiment was used to determine the antibiotic effect of bug plant extracts on dusky bug whereas Multi-choice experiment to determine the antixenosis/ repellent property of botanicals. It is evident from the results that mortality and antibiosis percentage of dusky bug due to the use of botanicals ranged from 15-95% and 20-87.3% respectively that was maximum in tobacoo extract followed by bakain and kurtama, minimum was on Ak, kanair and bakain extract. Non preference ranged from 14.28 to 85.7 where maximum non preference of dusky bug was found on bakain and kurtama followed by ak and kanair however minimum was on Bari pata extract. It was further found that local plant extract possessed insecticidal property toward dusky bug as well as also possesses repellency effect toward dusky bug, thus should be included in integrated pest management program of cotton in order to minimize the ill effects of pesticides it is compulsory to adopt eco-friendly methods of insect pest management.

Keywords: botanical extract, insecticidal and repellency activity, Gossypium hirsutum, oxycarenus laetus

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Authors: Ninlawat Phuangchoke, Waraporn Viyanon, Setta Sasananan

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The most important process of the water treatment plant process is the coagulation using alum and poly aluminum chloride (PACL), and the value of usage per day is a hundred thousand baht. Therefore, determining the dosage of alum and PACL are the most important factors to be prescribed. Water production is economical and valuable. This research applies an artificial neural network (ANN), which uses the Levenberg–Marquardt algorithm to create a mathematical model (Soft Jar Test) for prediction chemical dose used to coagulation such as alum and PACL, which input data consists of turbidity, pH, alkalinity, conductivity, and, oxygen consumption (OC) of Bangkhen water treatment plant (BKWTP) Metropolitan Waterworks Authority. The data collected from 1 January 2019 to 31 December 2019 cover changing seasons of Thailand. The input data of ANN is divided into three groups training set, test set, and validation set, which the best model performance with a coefficient of determination and mean absolute error of alum are 0.73, 3.18, and PACL is 0.59, 3.21 respectively.

Keywords: soft jar test, jar test, water treatment plant process, artificial neural network

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Authors: Aree Thongpukdee, Chockpisit Thepsithar, Chuthalak Thammaso

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Use of plants grown in local area for edible has a long tradition in different culture. The indigenous knowledge such as usage of plants as vegetables by local people is risk to disappear when no records are done. In order to conserve and transfer this valuable heritage to the new generation, ethnobotanical study should be investigated and documented. The survey of vegetable plants traditionally used was carried out in the year 2012. Information was accumulated via questionnaires and oral interviewing from 100 people living in 36 villages of 9 districts in Amphoe Huai Mek, Kalasin, Thailand. Local plant names, utilized parts and preparation methods of the plants were recorded. Each mentioned plant species were collected and voucher specimens were prepared. A total of 55 vegetable plant species belonging to 34 families and 54 genera were identified. The plant habits were tree, shrub, herb, climber, and shrubby fern at 21.82%, 18.18%, 38.18%, 20.00% and 1.82% respectively. The most encountered vegetable plant families were Leguminosae (20%), Cucurbitaceae (7.27%), Apiaceae (5.45%), whereas families with 3.64% uses were Araceae, Bignoniaceae, Lamiaceae, Passifloraceae, Piperaceae and Solanaceae. The most common consumptions were fresh or brief boiled young shoot or young leaf as side dishes of ‘jaeo, laab, namprik, pon’ or curries. Most locally known vegetables included 45% of the studied plants which grow along road side, backyard garden, hedgerow, open forest and rice field.

Keywords: vegetable plants, ethnobotanical survey, Kalasin, Thailand

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Authors: Maged El-Sayed Mohamed

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Plant tissue culture practices are presented nowadays as the most promising substitute to a whole plant in the terms of secondary metabolites production. They offer the advantages of high production, tunability and they have less effect on plant ecosystems. Lantana camara is a weed, which is common all over the world as an ornamental plant. Weeds can adapt to any type of soil and climate due to their rich cellular machinery for secondary metabolites’ production. This characteristic is found in Lantana camara as a plant of very rich diversity of secondary metabolites with no dominant class of compounds. Aim: This trait has encouraged the author to develop tissue culture experiments for Lantana camara to be a platform for production and manipulation of secondary metabolites through biotransformation. Methodology: The plant was collected in its flowering stage in September 2014, from which explants were prepared from shoot tip, auxiliary bud and leaf. Different types of culture media were tried as well as four phytohormones and their combinations; NAA, 2,4-D, BAP and kinetin. Explants were grown in dark or in 12 hours dark and light cycles at 25°C. A metabolic profile for the produced callus was made and then compared to the whole plant profile. The metabolic profile was made using GC-MS for volatile constituents (extracted by n-hexane) and by HPLC-MS and capillary electrophoresis-mass spectrometry (CE-MS) for non-volatile constituents (extracted by ethanol and water). Results: The best conditions for the callus induction was achieved using MS media supplied with 30 gm sucrose and NAA/BAP (1:0.2 mg/L). Initiation of callus was favoured by incubation in dark for 20 day. The callus produced under these conditions showed yellow colour, which changed to brownish after 30 days. The rate of callus growth was high, expressed in the callus diameter, which reached to 1.15±0.2 cm in 30 days; however, the induction of callus delayed for 15 days. The metabolic profile for both volatile and non-volatile constituents of callus showed more simple background metabolites than the whole plant with two new (unresolved) peaks in the callus’ nonvolatile constituents’ chromatogram. Conclusion: Lantana camara callus production can be itself a source of new secondary metabolites and could be used for biotransformation studies due to its simple metabolic background, which allow easy identification of newly formed metabolites. The callus production gathered the simple metabolic background with the rich cellular secondary metabolite machinery of the plant, which could be elicited to produce valuable medicinally active products.

Keywords: capillary electrophoresis-mass spectrometry, gas chromatography, metabolic profile, plant tissue culture

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Authors: Raviraja Shetty G., K. G. Poojitha

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An experiment was conducted at College of Horticulture, Mudigere to study the effect of different growth regulators on seed germination and vegetative propagation by cuttings of Celastrus paniculata an endangered medicinal plant. The extracted seeds are subjected to 11 different pre-soaking treatments which include control, GA3 at 300, 350, 400ppm, KNO3 at 1.0%, 1.5%, 2.0%, H2SO4 at 0.5%, 1.0% and HCl 0.5%,1.0% for 100 seeds per treatment. Among the different germination inducing treatments, seeds treated with gibberellins responded well with high seed germination and vigorous seedling growth. The seeds treated with GA3 400 ppm recorded maximum germination and growth parameters like rate of germination, shoot length, root length, plant vigour, fresh and dry weight of which was followed GA3 350 ppm. The commencement of germination and 50 per cent germination was also earlier in the same treatment. The cuttings of C. paniculata took more time for root initiation up to four months and sprouting percent was moderate as compared to other easy to root species. Among different treatments, IBA 2000 ppm was found to be the best, which recorded the maximum shoot and also root parameters. The results of present investigation will be helpful for conservation of this endangered medicinal plant through propagation

Keywords: conservation, germination, growth, germination, propagation

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Authors: M. J. Reis Lima, J. Oliveira, A. C. Sousa Pereira, M. C. Castilho, E. Teixeira-Lemos

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The increasing interest in plant sterol enriched foods is due to the fact that they reduce blood cholesterol concentrations without adverse side effects. In this context, enriched foods with phytosterols may be helpful in protecting population against atherosclerosis and cardiovascular diseases. The aim of the present work was to evaluate in a population of Viseu, Portugal, the consumption habits low-fat, plant sterol-enriched yoghurt. For this study, 577 inquiries were made and the sample was randomly selected for people shopping in various supermarkets. The preliminary results showed that the biggest consumers of these products were women aged 45 to 65 years old. Most of the people who claimed to buy these products consumed them once a day. Also, most of the consumers under antidyslipidemic therapeutics noticed positive effects on hypercholesterolemia.

Keywords: consumption habits, fermented milk, functional foods, low fat, phytosterols

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Authors: Damini Thawait, S. K. Dwivedi, Amit K. Patel, Samaptika Kar

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The experiment was carried out at Raipur during season of 2012 to find out the optimum planting patterns for scented rice cultivation. The treatment (T2) planting of two to three seedlings hill-1 transplanted in the spacing of 25 cm from plant to plant and 25 cm from row to row recorded significantly good grain quality i.e. higher head rice recovery (41.41) along with higher gain length (8.05).

Keywords: rice, scented, quality, yield

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Authors: Mariann Veresne Somosi, Zoltan Nagy, Krisztina Varga

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Innovation is the key element of economic development and a key factor in social processes. Technical innovations can be identified as prerequisites and causes of social change and cannot be created without the renewal of society. The study of social innovation can be characterised as one of the significant research areas of our day. The study’s aim is to identify the process of social innovation, which can be defined by input, transformation, and output factors. This approach divides the social innovation process into three parts: situation analysis, implementation, follow-up. The methods associated with each stage of the process are illustrated by the chronological line of social innovation. In this study, we have sought to present methodologies that support long- and short-term decision-making that is easy to apply, have different complementary content, and are well visualised for different user groups. When applying the methods, the reference objects are different: county, district, settlement, specific organisation. The solution proposed by the study supports the development of a methodological combination adapted to different situations. Having reviewed metric and conceptualisation issues, we wanted to develop a methodological combination along with a change management logic suitable for structured support to the generation of social innovation in the case of a locality or a specific organisation. In addition to a theoretical summary, in the second part of the study, we want to give a non-exhaustive picture of the two counties located in the north-eastern part of Hungary through specific analyses and case descriptions.

Keywords: factors of social innovation, methodological combination, social innovation process, supporting decision-making

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Authors: Priyal Motwani

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The current market for bamboo products in India is about Rs. 21000 crores and is highly unorganised and fragmented. In this study, we have closely analysed the structure and functions of a major bamboo craft based organisation in Kerela, India and elaborated about its value chain, product mix, pricing strategy and supply chain, collaborations and competitive landscape. We have identified six major bottlenecks that are prevalent in such organisations, based on the Indian context, in relation to their product mix, asset management, and supply chain- corresponding waste management and retail network. The study has identified that the target customers for the bamboo based products and alternative revenue streams (eco-tourism, microenterprises, training), by carrying out secondary and primary research (5000 sample space), that can boost the existing revenue by 150%. We have then recommended an optimum product mix-covering premium, medium and low valued processing, for medium sized bamboo based organisations, in accordance with their capacity to maximize their revenue potential. After studying such organisations and their counter parts, the study has established an optimum retail network, considering B2B, B2C physical and online retail, to maximize their sales to their target groups. On the basis of the results obtained from the analysis of the future and present trends, our study gives recommendations to improve the revenue potential of bamboo based organisation in India and promote sustainability.

Keywords: bamboo, bottlenecks, optimization, product mix, retail network, value chain

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Authors: Radu Pop, Adrian Bot, Vasile Rednic, Emil Bruj, Oana Raita, Liviu Vaida

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Our research presents a study concerning optimization of water flow capture for micro-hydro power plants in order to increase the energy production. It is known that the fish ladder whole, were the water is capture is fix, and the water flow may vary with the river flow, this means that on the fish ladder we will have different servitude flows, sometimes more than needed. We propose to demonstrate that the ‘winter intake’ from micro-hydro power plant, could be automated with an intelligent system which is capable to read some imposed data and adjust the flow in to the needed value. With this automation concept, we demonstrate that the performance of the micro-hydro power plant could increase, in some flow operating regimes, with approx. 10%.

Keywords: energy, micro-hydro, water intake, fish ladder

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Authors: Muhammad Naeem Chaudhry, Fahim Nawaz, Rana Nauman Shabbir

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New strategies aimed at increasing the resilience of crop plants to the negative effects of climate change represent important research priorities of plant scientists. The use of soil microorganisms to alleviate abiotic stresses like drought has gained particular importance in recent past. A field experiment was planned to investigate the effect of phosphorous solubilizing bacteria on yield and seed quality of Camelina (Camelina sativa L.) under water deficit conditions. The study was conducted at Agronomic Research Farm, University College of Agriculture and Environmental Sciences, The Islamia University Bahawalpur, during 4th week of November, 2013. The available seeds of Camelina sativa were inoculated with two bacterial strains (pseudomonas and Bacillus spp.) and grown under various water stress levels i.e. D0, (four irrigations), D3 (three irrigation), D2 (two irrigations), and D1 (one irrigation). The results revealed that drought stress significantly reduced the plant growth and yield, consequently reducing protein contents and oil concentration in camelina. The exposure to drought stress decreased plant height (16%), plant population (27%), number of fertile branches (41-59%), number of pods per plant (35%) and seed per pod (33%). Drought stress also exerted a negative impact on yield characteristics by reducing the 1000-seed weight (65%), final seed yield (52%), biological yield (22%) and harvest index (39%) of camelina. However, the inoculation of seeds with Pseudomonas and Bacillus spp. promoted the plant growth characterized by increased plant height and enhanced plant population. It was noted that inoculation of seeds with Pseudomonas resulted in the maximum plant population (113.4 cm), primary branches (19 plant-1), and number of pods (664 plant-1), whereas Bacillus inoculation resulted in maximum plant height (113.4 cm), seeds per pod (15.9), 1000-seed weight (1.85 g), and seed yield (3378.8 kg ha-1). Moreover, the inoculation with Bacillus also significantly improved the quality attributes of camelina and gave 3.5% and 2.1% higher oil contents than Pseudomonas and control (no-inoculation), respectively. Similarly, the same strain also resulted in maximum protein contents (33.3%). Our results confirmed the hypothesis that inoculation of seeds with phosphorous solubilizing bacterial strains is an effective, viable and environment-friendly approach to improve yield and quality of camelina under water deficit conditions. However, further studies are suggested to investigate the physiological and molecular processes, stimulated by bacterial strains, for increasing drought tolerance in food crops.

Keywords: Camelina, drought stress, phosphate solubilizing bacteria, seed quality

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Authors: Jialin Ma, Jia Meng

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Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications.

Keywords: RNA-related genomic features, annotation, visualization, web server

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Authors: Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto

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Site-directed mutagenesis is a renowned technique to introduce specific mutations in the genome. To achieve site-directed mutagenesis, many chemical and enzymatic approaches have been reported in the past like disulphite induced genome editing, CRISPR-Cas9, TALEN etc. The chemical methods are invasive whereas the enzymatic approaches are time-consuming and expensive. Most of these techniques are unusable in the cellular application due to their toxicity and other limitations. Photo-chemical cytosine deamination, introduced in 2010, is one of the major technique for enzyme-free single-point mutation of cytosine to uracil in DNA and RNA, wherein, 3-cyanovinylcarbazole nucleoside (CNVK) containing oligodeoxyribonucleotide (ODN) having CNVK at -1 position to that of target cytosine is reversibly crosslinked to target DNA strand using 366 nm and then incubated at 90ºC to accommodate deamination. This technique is superior to enzymatic methods of site-directed mutagenesis but has a disadvantage that it requires the use of high temperature for the deamination step which restricts its applicability in the in vivo applications. This study has been focused on improving the technique by reducing the temperature required for deamination. Firstly, the photo-cross-linker, CNVK has been modified by replacing cyano group attached to vinyl group with methyl ester (OMeVK), amide (NH2VK), and carboxylic acid (OHVK) to observe the acceleration in the deamination of target cytosine cross-linked to vinylcarbazole derivative. Among the derivatives, OHVK has shown 2 times acceleration in deamination reaction as compared to CNVK, while the other two derivatives have shown deceleration towards deamination reaction. The trend of rate of deamination reaction follows the same order as that of hydrophilicity of the vinylcarbazole derivatives. OHVK being most hydrophilic has shown highest acceleration while OMeVK is least hydrophilic has proven to be least active for deamination. Secondly, in the related study, the counter-base of the target cytosine, guanine has been replaced by inosine, 2-aminopurine, nebularine, and 5-nitroindole having distinct hydrogen bonding patterns with target cytosine. Among the ODNs with these counter bases, ODN with inosine has shown 12 fold acceleration towards deamination of cytosine cross-linked to CNVK at physiological conditions as compared to guanosine. Whereas, when 2-aminopurine, nebularine, and 5-nitroindole were used, no deamination reaction took place. It can be concluded that inosine has potential to be used as the counter base of target cytosine for the CNVK mediated photo-cross-linking induced deamination of cytosine. The increase in rate of deamination reaction has been attributed to pattern and number of hydrogen bonding between the cytosine and counter base. One of the important factor is presence of hydrogen bond between exo-cyclic amino group of cytosine and the counter base. These results will be useful for development of more efficient technique for site-directed mutagenesis for C → U transformations in the DNA/RNA which might be used in the living system for treatment of various genetic disorders and genome engineering for making designer and non-native proteins.

Keywords: C to U transformation, DNA editing, genome engineering, ultra-fast photo-cross-linking

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Authors: Munir Rusan

Abstract:

Municipal waste management (MWM) represents a cornerstone in the effort to preserve the environment, which guarantees a healthy living environment for communities. MWM is directly affected by population growth and population density, urbanization, and tourism. In Jordan, MWM is currently managed by transferring and dumping waste into landfills. Landfills are mostly saturated and cannot receive any more waste. Besides, the organic waste, which accounts for 50% of municipal waste, will be naturally fermented in the landfills creating an unpleasant odor and emits greenhouse gases as well as generate organic leachates that are harmful to the environment. Organic waste can be aerobically composted and generate organic fertilizer called compost. Compost is very beneficial to soil and plant growth and, in general, to the ecosystem. Home composting is very common in most developed countries, but unfortunately, in developing countries such as Jordan, such an approach is not practiced and is not even socially well acceptable. The objective of this study was to evaluate the physical and chemical properties of home composting materials and to produce compost for further use as a soil amendment. The effect of compost soil application on the soil-plant system was evaluated. The soil application of the compost resulted in enhancing soil organic matter and soil N, P, and K content. The plant growth was also improved quantitatively and qualitatively. It was concluded that composting of municipal organic solid waste and soil application of the compost has a significant positive impact on the environment and soil-plant productivity.

Keywords: composting, organic solid waste, soil, plant

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Authors: M. Wigwe, J. G Akpa, E. N Wami

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Mathematical models of the absorber of a glycol dehydration facility was developed using the principles of conservation of mass and energy. Models which predict variation of the water content of gas in mole fraction, variation of gas and liquid temperatures across the parking height were developed. These models contain contributions from bulk and diffusion flows. The effect of diffusion on the process occurring in the absorber was studied in this work. The models were validated using the initial conditions in the plant data from Company W TEG unit in Nigeria. The results obtained showed that the effect of diffusion was noticed between z=0 and z=0.004 m. A deviation from plant data of 0% was observed for the gas water content at a residence time of 20 seconds, at z=0.004 m. Similarly, deviations of 1.584% and 2.844% were observed for the gas and TEG temperatures.

Keywords: separations, absorption, simulation, dehydration, water content, triethylene glycol

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Authors: Amin Rezazadeh, Parisa Farahpour, Arezoo Rezazadeh, Morteza Sam Deliri

Abstract:

In order to investigate the effects of nitrogen and compost different levels on qualitative and quantitative performance of Calendula officinalis L. herb, an experiment was carried out in the research field of Chalous Azad University in 2011-2012. The experiment was done in factorial form as a randomized complete block design, in three replicates. Treatments consisted of nitrogen and compost. Considered nitrogen levels consisted of N0=0, N1=50, N2=100 kg/ha and compost levels were including C0=0, C1=6, C2=12 ton/ha. Investigated characteristics consisted of flower dry weight, number of flowers in plant, flower diameter. The results showed, nitrogen and compost treatments had statistically significant influence (p ≤ 0.01) on studied characteristics. Flower dry weight, flower diameter and number of flower in plant characteristics has been studied in four harvest; as, the performance of these characteristics had increasing procedure from the first harvest up to the forth harvest; and, in the fourth harvest, it has reached to its` maximum level. As, up to the forth harvest, the maximum flower dry weight, flower diameter and number of flower in plant obtained by C1× N2 (C1=6 ton/ha compost and N2=100 kg/ha nitrogen) treatment.

Keywords: calendula, compost, nitrogen, flavonoid

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Authors: Mishari Khajah, Mohd. Elmuntasir Ahmed, Abdullah Al-Matouq, Farah Al-Ajeel, Fatemah Dashti, Ahmed Shishter

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The overall aim of this study was to monitor and evaluate the effluent quality of a reverse osmosis (RO) reject wastewater from the biggest wastewater treatment plant in the world that is using RO and ultrafiltration membranes in their processes to reclaim water for indirect potable water reuse from municipal wastewaters. The RO reject wastewater or brine included various contaminants that could harm the human health and the environment such as trace organics, organic matters, heavy metals, nutrients and pathogens. Unfortunately, there are no legally binding regulatory guidelines for brine management in Kuwait as many countries around the world. This study monitors and evaluate the RO reject wastewater (brine) generated from the Sulaibiya Wastewater Treatment Plant. Samples were collected and analyzed about 37 parameters for one-year period, twice a month, and compare it to Kuwait Environment Public Authority, KEPA. Results showed that the heavy metals parameters were above KEPA standards, which needs to be treated.

Keywords: domestic wastewater, management, potable water, RO reject wastewater, Sulaibiya wastewater treatment plant

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Authors: Maria Manzoor, Iram Gul, Muhammad Arshad

Abstract:

Bacterial strains were isolated from contaminated soil collected from Rawalpindi and Islamabad. The strains were investigated for lead resistance and their effect on Pb solubility and PGPR activity. Incubation experiments were carried for inoculated and unoculated soil containing different levels of Pb. Results revealed that few stains (BTM-4, BTM-11, BTM-14) were able to tolerate Pb up to 600 mg L-1, whereas five strains (BTM-3, BTM-6, BTM-10, BTM-21 and BTM-24) showed significant increase in solubility of Pb when compared to all other strains and control. The CaCl2 extractable Pb was increased by 13.6, 6.8, 4.4 and 2.4 folds compared to un-inoculated control soil at increased soil Pb concentration (500, 1000, 1500 and 200 mg kg-1, respectively). The selected bacterial strains (11) were further investigated for plant growth promotion activity through PGPR assays including. Germination and root elongation assays were also conducted under elevated metal concentration in controlled conditions to elucidate the effects of microbial strains upon plant growth and development. The results showed that all the strains tested in this study, produced significantly varying concentrations of IAA, siderophores and gibberellic acid along with ability to phosphorus solubilization index (PSI). The results of germination and root elongation assay further confirmed the beneficial role of the microbial strains in elevating metal stress through PGPR activity. Among all tested strains, BTM-10 significantly improved plant growth. 1.3 and 2.7 folds increase in root and shoot length was observed when compared to control. Which may be attributed to presence of important plant growth promoting enzymes (IAA 74.6 μg/ml; GA 19.23 μg/ml; Sidrophore units 49% and PSI 1.3 cm). The outcome of this study indicates that these Pb tolerant and solubilizing strains may have the potential for plant growth promotion under metal stress and can be used as mediator when coupled with heavy metal hyperaccumulator plants for phytoremediation of Pb contaminated soil.

Keywords: Pb resistant bacteria, Pb mobilizing bacteria, Phytoextraction of Pb, PGPR activity of bacteria

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Authors: Nabil Hameed Al-Farsi

Abstract:

This study’s main goal is to develop a model and a maintenance strategy for a cement factory called Arabian Cement Company, Rabigh Plant. The proposed work here depends on Reliability centric maintenance approach to develop a strategy and maintenance schedule that ensures increasing the reliability of the production system components, thus ensuring continuous productivity. The cost-effective maintenance of the plant’s dependability performance is the key goal of durability-based maintenance is. The cement plant consists of 7 important steps, so, developing a maintenance plan based on Reliability centric maintenance (RCM) method is made up of 10 steps accordingly starting from selecting units and data until performing and updating the model. The processing unit chosen for the analysis of this case is the calcinatory unit regarding model’s validation and the Travancore Titanium Products Ltd (TTP) using the claimed data history acquired from the maintenance department maintenance from the mentioned company. After applying the proposed model, the results of the maintenance simulation justified the plant's existing scheduled maintenance policy being reconsidered. Results represent the need for preventive maintenance for all Class A criticality equipment instead of the planned maintenance and the breakdown one for all other equipment depends on its criticality and an FMEA report. Consequently, the additional cost of preventive maintenance would be offset by the cost savings from breakdown maintenance for the remaining equipment.

Keywords: engineering, reliability, strategy, maintenance, failure modes, effects and criticality analysis (FMEA)

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Authors: Sridhar A. Malkaram, Tamer E. Fandy

Abstract:

Purpose: 5-Azacytidine (5AC) and decitabine (DC) are DNA hypomethylating agents. We recently demonstrated that both drugs increase the enzymatic activity of the histone deacetylase enzyme SIRT6. Accordingly, we are comparing the changes H3K9 acetylation changes in the whole genome induced by both drugs using leukemia cells. Description of Methods & Materials: Mononuclear cells from the bone marrow of six de-identified naive acute myeloid leukemia (AML) patients were cultured with either 500 nM of DC or 5AC for 72 h followed by ChIP-Seq analysis using a ChIP-validated acetylated-H3K9 (H3K9ac) antibody. Chip-Seq libraries were prepared from treated and untreated cells using SMARTer ThruPLEX DNA- seq kit (Takara Bio, USA) according to the manufacturer’s instructions. Libraries were purified and size-selected with AMPure XP beads at 1:1 (v/v) ratio. All libraries were pooled prior to sequencing on an Illumina HiSeq 1500. The dual-indexed single-read Rapid Run was performed with 1x120 cycles at 5 pM final concentration of the library pool. Sequence reads with average Phred quality < 20, with length < 35bp, PCR duplicates, and those aligning to blacklisted regions of the genome were filtered out using Trim Galore v0.4.4 and cutadapt v1.18. Reads were aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in end-to-end alignment mode. H3K9ac enriched (peak) regions were identified using diffReps v1.55.4 software using input samples for background correction. The statistical significance of differential peak counts was assessed using a negative binomial test using all individuals as replicates. Data & Results: The data from the six patients showed significant (Padj<0.05) acetylation changes at 925 loci after 5AC treatment versus 182 loci after DC treatment. Both drugs induced H3K9 acetylation changes at different chromosomal regions, including promoters, coding exons, introns, and distal intergenic regions. Ten common genes showed H3K9 acetylation changes by both drugs. Approximately 84% of the genes showed an H3K9 acetylation decrease by 5AC versus 54% only by DC. Figures 1 and 2 show the heatmaps for the top 100 genes and the 99 genes showing H3K9 acetylation decrease after 5AC treatment and DC treatment, respectively. Conclusion: Despite the similarity in hypomethylating activity and chemical structure, the effect of both drugs on H3K9 acetylation change was significantly different. More changes in H3K9 acetylation were observed after 5 AC treatments compared to DC. The impact of these changes on gene expression and the clinical efficacy of these drugs requires further investigation.

Keywords: DNA methylation, leukemia, decitabine, 5-Azacytidine, epigenetics

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Authors: Zia Amjad, Salem Safar Alghamdi

Abstract:

This experiment was carried out at student educational farm College of Food and Agriculture, KSU, kingdom of Saudi Arabia; in order to characterize 154 Vicia faba, characterization, PCA, ago-morphological diversity. Icia faba L. accessions were based on ipove and ibpgr descriptors. 24 agro-morphological characters including 11 quantitative and 13 qualitative were observed for genetic variation. All the results were analyzed using multivariate analysis i.e. principle component analysis. First 6 principle components with eigenvalue greater than one; accounted for 72% of available Vicia faba genetic diversity. However, first three components revealed more than 10% of genetic diversity each i.e. 22.36%, 15.86%, and 10.89% respectively. PCA distributed the V. faba accessions into different groups based on their performance for the characters under observation. PC-1 which represented 22.36% of the genetic diversity was positively associated with stipule spot pigmentation, intensity of streaks, pod degree of curvature and to some extent with 100 seed weight. PC-2 covered 15.86 of the genetic diversity and showed positive association for average seed weight per plant, pod length, number of seeds per plant, 100 seed weight, stipule spot pigmentation, intensity of streaks (same as in PC-1), and to some extent for pod degree of curvature and number of pods per plant. PC-3 revealed 10.89% of genetic diversity and expressed positive association for number of pods per plant and number of leaflets per plant.

Keywords: Vicia faba, characterization, PCA, ago-morphological diversity

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Authors: Biskri Yasmina, Laidi Babouri, Dehas Ouided, Bougherira Nadjiba, Baghloul Rahima

Abstract:

Algeria is one of the countries which have extraordinary resources in vegetable fibers (Palmier, Alfa, Cotton, Sisal). Unfortunately, their valorization in the practical fields, among other things, in building materials, is still little exploited. Several works align with the fact that the use of plant fibers in mortar is an advantageous solution, given its abundance and its socio-economic and environmental impact. The idea of introducing plant fiber into the field of Civil Engineering is not new. Based on the work of several researchers in this field, we propose to study the mechanical behavior of mortar based on Sisal fibers. This work consists of the experimental characterization in the fresh state (workability) and in the hardened state (mechanical resistance to compression and traction by three-point bending) on the scale of mortar mortars based on sisal plant fibers. The main objective of this work is the study of the effect of fiber incorporation on mechanical properties (compressive strength and three-point bending strength). In this study, we varied two parameters, such as the length of the fiber (7cm, 10 cm) and the fibers percentage (0.25%, 0.5%, 0.75%, 1%, 1.25% and 1.5%). The results show that there is a slight increase in the compressive strength of the fiber-reinforced mortars compared to the reference mortar (mortar without fibers). With regard to the three-point bending tests, the fiber-reinforced mortars presented higher resistances compared to the reference mortar and this was for the different lengths and different percentages studied.

Keywords: mortar, plant fiber, experimentation, mechanical characterization, analysis

Procedia PDF Downloads 55