Search results for: Endemic species

Authors: Esam Jassim

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Industries using conventional fossil fuels have an  interest in better understanding the mechanism of particulate  formation during combustion since such is responsible for emission  of undesired inorganic elements that directly impact the atmospheric  pollution level. Fine and ultrafine particulates have tendency to  escape the flue gas cleaning devices to the atmosphere. They also  preferentially collect on surfaces in power systems resulting in  ascending in corrosion inclination, descending in the heat transfer  thermal unit, and severe impact on human health. This adverseness  manifests particularly in the regions of world where coal is the  dominated source of energy for consumption.  This study highlights the behavior of calcium transformation as  mineral grains verses organically associated inorganic components  during pulverized coal combustion. The influence of existing type of  calcium on the coarse, fine and ultrafine mode formation mechanisms  is also presented. The impact of two sub-bituminous coals on particle  size and calcium composition evolution during combustion is to be  assessed. Three mixed blends named Blends 1, 2, and 3 are selected  according to the ration of coal A to coal B by weight. Calcium  percentage in original coal increases as going from Blend 1 to 3.  A mathematical model and a new approach of describing  constituent distribution are proposed. Analysis of experiments of  calcium distribution in ash is also modeled using Poisson distribution.  A novel parameter, called elemental index λ, is introduced as a  measuring factor of element distribution.  Results show that calcium in ash that originally in coal as mineral  grains has index of 17, whereas organically associated calcium  transformed to fly ash shown to be best described when elemental  index λ is 7.  As an alkaline-earth element, calcium is considered the  fundamental element responsible for boiler deficiency since it is the  major player in the mechanism of ash slagging process. The  mechanism of particle size distribution and mineral species of ash  particles are presented using CCSEM and size-segregated ash  characteristics. Conclusions are drawn from the analysis of  pulverized coal ash generated from a utility-scale boiler.

 

Keywords: Calcium transformation, Coal Combustion, Inorganic Element, Poisson distribution.

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Authors: S. Al-Khalasi, O. Mahgoub, H. Yaakub

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This study evaluated the use of raw or processed Prosopis juliflora (Meskit) pods as a major ingredient in a formulated ration to provide an alternative non-conventional concentrate for livestock feeding in Oman. Dry Meskit pods were reduced to lengths of 0.5- 1.0 cm to ensure thorough mixing into three diets. Meskit pods were subjected to two types of treatments; roasting and soaking. They were roasted at 150оC for 30 minutes using a locally-made roasting device (40 kg barrel container rotated by electric motor and heated by flame gas cooker). Chopped pods were soaked in tap water for 24 hours and dried for 2 days under the sun with frequent turning. The Meskit-pod-based diets (MPBD) were formulated and pelleted from 500 g/kg ground Meskit pods, 240 g/kg wheat bran, 200 g/kg barley grain, 50 g/kg local dried sardines and 10 g/kg of salt. Twenty four 10 months-old intact Omani male lambs with average body weight of 27.3 kg (± 0.5 kg) were used in a feeding trial for 84 days. They were divided (on body weight basis) and allocated to four diet combination groups. These were: Rhodes grass hay (RGH) plus a general ruminant concentrate (GRC); RGH plus raw Meskit pods (RMP) based concentrate; RGH plus roasted Meskit pods (ROMP) based concentrate; RGH plus soaked Meskit pods (SMP) based concentrate Daily feed intakes and bi-weekly body weights were recorded. MPBD had higher contents of crude protein (CP), acid detergent fibre (ADF) and neutral detergent fibre (NDF) than the GRC. Animals fed various types of MPBD did not show signs of ill health. There was a significant effect of feeding ROMP on the performance of Omani sheep compared to RMP and SMP. The ROMP fed animals had similar performance to those fed the GRC in terms of feed intake, body weight gain and feed conversion ratio (FCR).This study indicated that roasted Meskit pods based diet may be used instead of the commercial concentrate for feeding Omani sheep without adverse effects on performance. It offers a cheap alternative source of protein and energy for feeding Omani sheep. Also, it might help in solving the spread impact of Meskit trees, maintain the ecosystem and helping in preserving the local tree species.

Keywords: Growth, Meskit, Omani sheep, Prosopis juliflora.

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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Authors: Siti Aisya Gany, Swee Ching Tan, Sook Yee Gan

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Diminished antioxidant defense or increased production of reactive oxygen species in the biological system can result in oxidative stress which may lead to various neurodegenerative diseases including Alzheimer’s disease (AD). Microglial activation also contributes to the progression of AD by producing several proinflammatory cytokines, nitric oxide (NO) and prostaglandin E2 (PGE2). Oxidative stress and inflammation have been reported to be possible pathophysiological mechanisms underlying AD. In addition, the cholinergic hypothesis postulates that memory impairment in patient with AD is also associated with the deficit of cholinergic function in the brain. Although a number of drugs have been approved for the treatment of AD, most of these synthetic drugs have diverse side effects and yield relatively modest benefits. Marine algae have great potential in pharmaceutical and biomedical applications as they are valuable sources of bioactive properties such as anticoagulation, antimicrobial, antioxidative, anticancer and anti-inflammatory. Hence, this study aimed to provide an overview of the properties of Malaysian seaweeds (Padina australis, Sargassum polycystum and Caulerpa racemosa) in inhibiting oxidative stress, neuroinflammation and cholinesterase enzymes. These seaweeds significantly exhibited potent DPPH and moderate superoxide anion radical scavenging ability (P<0.05). Hexane and methanol extracts of S. polycystum exhibited the most potent radical scavenging ability with IC50 values of 0.157±0.004mg/ml and 0.849±0.02mg/ml for DPPH and ABTS assays, respectively. Hexane extract of C. racemosa gave the strongest superoxide radical inhibitory effect (IC50 of 0.386±0.01mg/ml). Most seaweed extracts significantly inhibited the production of cytokine (IL-6, IL-1 β, TNFα) and NO in a concentration-dependent manner without causing significant cytotoxicity to the lipopolysaccharide (LPS)-stimulated microglia cells (P<0.05). All extracts suppressed cytokine and NO level by more than 50% at the concentration of 0.4mg/ml. In addition, C. racemosa and S. polycystum also showed anti-acetylcholinesterase activities with the IC50 values ranging from 0.086-0.115 mg/ml. Moreover, C. racemosa and P. australis were also found to be active against butyrylcholinesterase with IC50 values ranging from 0.118- 0.287 mg/ml.

Keywords: Anticholinesterase, antioxidative, neuroinflammation, seaweeds.

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Authors: U. K. Hulihalli, Shantveerayya

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Buckwheat (Fagopyrum esculentum Moench) is an annual crop belongs to family Poligonaceae. The cultivated buckwheat species are notable for their exceptional nutritive values. It is an important source of carbohydrates, fibre, macro, and microelements such as K, Ca, Mg, Na and Mn, Zn, Se, and Cu. It also contains rutin, flavonoids, riboflavin, pyridoxine and many amino acids which have beneficial effects on human health, including lowering both blood lipid and sugar levels. Rutin, quercetin and some other polyphenols are potent carcinogens against colon and other cancers. Buckwheat has significant nutritive value and plenty of uses. Cultivation of buckwheat in Sothern part of India is very meager. Hence, a study was planned with an objective to know the performance of buckwheat genotypes to different planting geometries and fertility levels. The field experiment was conducted at Main Agriculture Research Station, University of Agriculture Sciences, Dharwad, India, during 2017 Kharif. The experiment was laid-out in split-plot design with three replications having three planting geometries as main plots, two genotypes as sub plots and three fertility levels as sub-sub plot treatments. The soil of the experimental site was vertisol. The standard procedures are followed to record the observations. The planting geometry of 30*10 cm was recorded significantly higher seed yield (893 kg/ha⁻¹), stover yield (1507 kg ha⁻¹), clusters plant⁻¹ (7.4), seeds clusters⁻¹ (7.9) and 1000 seed weight (26.1 g) as compared to 40*10 cm and 20*10 cm planting geometries. Between the genotypes, significantly higher seed yield (943 kg ha⁻¹) and harvest index (45.1) was observed with genotype IC-79147 as compared to PRB-1 genotype (687 kg ha⁻¹ and 34.2, respectively). However, the genotype PRB-1 recorded significantly higher stover yield (1344 kg ha⁻¹) as compared to genotype IC-79147 (1173 kg ha⁻¹). The genotype IC-79147 was recorded significantly higher clusters plant⁻¹ (7.1), seeds clusters⁻¹ (7.9) and 1000 seed weight (24.5 g) as compared PRB-1 (5.4, 5.8 and 22.3 g, respectively). Among the fertility levels tried, the fertility level of 60:30 NP kg ha⁻¹ recorded significantly higher seed yield (845 kg ha^-1) and stover yield (1359 kg ha⁻¹) as compared to 40:20 NP kg ha^-1 (808 and 1259 kg ha⁻¹ respectively) and 20:10 NP kg ha^-1 (793 and 1144 kg ha⁻¹ respectively). Within the treatment combinations, IC 79147 genotype having 30*10 cm planting geometry with 60:30 NP kg ha⁻¹ recorded significantly higher seed yield (1070 kg ha⁻¹), clusters plant⁻¹ (10.3), seeds clusters⁻¹ (9.9) and 1000 seed weight (27.3 g) compared to other treatment combinations.

Keywords: Buckwheat, fertility levels, genotypes, geometry, polyphenols, rutin.

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Authors: L. Gómez-Limia, I. Franco, T. Blanco, S. Martínez

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European eels (Anguilla anguilla) belong to Anguilliformes order and Anguillidae family. They are generally classified as warm-water fish. Eels have a great commercial value in Europe and Asian countries. Eels can reach high weights, although their commercial size is relatively low in some countries. The capture of larger eels would facilitate the recovery of the species, as well as having a greater number of either glass eels or elvers for aquaculture. In the last years, the demand and the price of eels have increased significantly. However, European eel is considered critically endangered by the International Union for the Conservation of Nature (IUCN) Red List. The biochemical composition of fishes is an important aspect of quality and affects the nutritional value and consumption quality of fish. In addition, knowing this composition can help predict an individual’s condition for their recovery. Fish is known to be important source of protein rich in essential amino acids. However, there is very little information about changes in amino acids composition of European eels with increase in size. The aim of this study was to evaluate the effect of two different weight categories on the amino acids content in muscle tissue of wild European eels. European eels were caught in River Ulla (Galicia, NW Spain), during winter. The eels were slaughtered in ice water immersion. Then, they were purchased and transferred to the laboratory. The eels were subdivided into two groups, according to the weight. The samples were kept frozen (-20 °C) until their analysis. Frozen eels were defrosted and the white muscle between the head and the anal hole. was extracted, in order to obtain amino acids composition. Thirty eels for each group were used. Liquid chromatography was used for separation and quantification of amino a cids. The results conclude that the eels are rich in glutamic acid, leucine, lysine, threonine, valine, isoleucine and phenylalanine. The analysis showed that there are significant differences (p < 0.05) among the eels with different sizes. Histidine, threonine, lysine, hydroxyproline, serine, glycine, arginine, alanine and proline were higher in small eels. European eels muscle presents between 45 and 46% of essential amino acids in the total amino acids. European eels have a well-balanced and high quality protein source in the respect of E/NE ratio. However, eels with higher weight showed a better ratio of essential and non-essential amino acid.

Keywords: European eels, amino acids, HPLC, body size.

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Authors: Mayank Singh, O. P. Singh ‘Vatsa’, M. P. Singh

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Present paper deals with an evaluation of magnitude of changes in biomass and net primary productivity at ‘Gujar Tal’ sloppy lake margin at Jaunpur in tropical semi-arid region of eastern U.P. (India). The study site abandoned or neglected lands (50 ×125 m) was divided into two zones, i.e. upper zone (up-land) and lower zone (low-land). Maximum biomass in the upper zone of dominant weed Desmostachya bipinnata (L.) Stapf. was 207.47 g m-2 and ‘rest weeds’ was 457.45 g m-2 both in the month of September. In contrast, the peak biomass value in the lower zone of dominant weed Oryza rufipogon Griff. was 1571.44 g m-2 in October and ‘rest weeds’ 270.65 g m-2 in February. Among the two zones, the peak total community biomass was observed 1655.62 g m-2 (October) in the lower zone while its peak value for the upper zone 457.45 g m-2 (September) was comparatively low. Maximum percentage contribution of dominant weeds (D. bipinnata and O. rufipogon) in the respective upper and lower zones and ‘rest weeds’ in both the zones varied in different months in the total community biomass. The peak net primary productivity of dominant weed (D. bipinnata) was 2.09g m-2 day-1 (September) and ‘rest weeds’ was 2.37 g m-2 day-1 (August) in the upper zone, while the lower zone for O. rufipogon was 5.25 g m-2 day-1 (June) as this zone was inundated later and ‘rest weeds’ was 2.08 g m-2 day-1 (January, 2009). The annual net production of total community at site I was highest, 409.58 g m-2 yr-1 in the upper zone followed by 395.58 g m-2 per eight month in the lower zone as this zone was flooded with water during rainy season. The site significance of variations in biomass in relation to plant species was tested by analysis of variance. It was significant between months in all the two zones (p<0.01 and p<0.05).

Keywords: Biomass, Neglected Lake Margin, Productivity, Vegetation.

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Authors: A. M. Tarola, R. Preti, A. M. Girelli, P. Campana

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Safeguarding, studying and enhancing biodiversity play an important and indispensable role in re-launching agriculture. The ancient local varieties are therefore a precious resource for genetic and health improvement. In order to protect biodiversity through the recovery and valorization of autochthonous varieties, in this study we analyzed 12 samples of four ancient apple cultivars representative of Friuli Venezia Giulia, selected by local farmers who work on a project for the recovery of ancient apple cultivars. The aim of this study is to evaluate the polyphenolic profile and the antioxidant capacity that characterize the organoleptic and functional qualities of this fruit species, besides having beneficial properties for health. In particular, for each variety, the following compounds were analyzed, both in the skins and in the pulp: gallic acid, catechin, chlorogenic acid, epicatechin, caffeic acid, coumaric acid, ferulic acid, rutin, phlorizin, phloretin and quercetin to highlight any differences in the edible parts of the apple. The analysis of individual phenolic compounds was performed by High Performance Liquid Chromatography (HPLC) coupled with a diode array UV detector (DAD), the antioxidant capacity was estimated using an in vitro essay based on a Free Radical Scavenging Method and the total phenolic compounds was determined using the Folin-Ciocalteau method. From the results, it is evident that the catechins are the most present polyphenols, reaching a value of 140-200 μg/g in the pulp and of 400-500 μg/g in the skin, with the prevalence of epicatechin. Catechins and phlorizin, a dihydrohalcone typical of apples, are always contained in larger quantities in the peel. Total phenolic compounds content was positively correlated with antioxidant activity in apple pulp (r² = 0,850) and peel (r² = 0,820). Comparing the results, differences between the varieties analyzed and between the edible parts (pulp and peel) of the apple were highlighted. In particular, apple peel is richer in polyphenolic compounds than pulp and flavonols are exclusively present in the peel. In conclusion, polyphenols, being antioxidant substances, have confirmed the benefits of fruit in the diet, especially as a prevention and treatment for degenerative diseases. They demonstrated to be also a good marker for the characterization of different apple cultivars. The importance of protecting biodiversity in agriculture was also highlighted through the exploitation of native products and ancient varieties of apples now forgotten.

Keywords: Apple, biodiversity, polyphenols, antioxidant activity, HPLC-DAD, characterization.

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Authors: Markus Nordlund, Arkadiusz K. Kuczaj

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Philip Morris International (PMI) is developing a range of novel tobacco products with the potential to reduce individual risk and population harm in comparison to smoking cigarettes. One of these products is the Tobacco Heating System 2.2 (THS 2.2), (named as the Electrically Heated Tobacco System (EHTS) in this paper), already commercialized in a number of countries (e.g., Japan, Italy, Switzerland, Russia, Portugal and Romania). During use, the patented EHTS heats a specifically designed tobacco product (Electrically Heated Tobacco Product (EHTP)) when inserted into a Holder (heating device). The EHTP contains tobacco material in the form of a porous plug that undergoes a controlled heating process to release chemical compounds into vapors, from which an aerosol is formed during cooling. The aim of this work was to investigate the aerosol formation characteristics for realistic operating conditions of the EHTS as well as for relevant gas mixture compositions measured in the EHTP aerosol consisting mostly of water, glycerol and nicotine, but also other compounds at much lower concentrations. The nucleation process taking place in the EHTP during use when operated in the Holder has therefore been modeled numerically using an extended Classical Nucleation Theory (CNT) for multicomponent gas mixtures. Results from the performed simulations demonstrate that aerosol droplets are formed only in the presence of an aerosol former being mainly glycerol. Minor compounds in the gas mixture were not able to reach a supersaturated state alone and therefore could not generate aerosol droplets from the multicomponent gas mixture at the operating conditions simulated. For the analytically characterized aerosol composition and estimated operating conditions of the EHTS and EHTP, glycerol was shown to be the main aerosol former triggering the nucleation process in the EHTP. This implies that according to the CNT, an aerosol former, such as glycerol needs to be present in the gas mixture for an aerosol to form under the tested operating conditions. To assess if these conclusions are sensitive to the initial amount of the minor compounds and to include and represent the total mass of the aerosol collected during the analytical aerosol characterization, simulations were carried out with initial masses of the minor compounds increased by as much as a factor of 500. Despite this extreme condition, no aerosol droplets were generated when glycerol, nicotine and water were treated as inert species and therefore not actively contributing to the nucleation process. This implies that according to the CNT, an aerosol cannot be generated without the help of an aerosol former, from the multicomponent gas mixtures at the compositions and operating conditions estimated for the EHTP, even if all minor compounds are released or generated in a single puff.

Keywords: Aerosol, Classical Nucleation Theory (CNT), Electrically Heated Tobacco Product (EHTP), Electrically Heated Tobacco System (EHTS), modeling, multicomponent, nucleation.

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Authors: Ali Zaker, Zhi Chen

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Due to the concerns about the depletion of fossil fuel sources and the deteriorating environment, the attempt to investigate the production of renewable energy will play a crucial role as a potential to alleviate the dependency on mineral fuels. One particular area of interest is generation of bio-oil through sewage sludge (SS) pyrolysis. SS can be a potential candidate in contrast to other types of biomasses due to its availability and low cost. However, the presence of high molecular weight hydrocarbons and oxygenated compounds in the SS bio-oil hinders some of its fuel applications. In this context, catalytic pyrolysis is another attainable route to upgrade bio-oil quality. Among different catalysts (i.e., zeolites) studied for SS pyrolysis, activated chars (AC) are eco-friendly alternatives. The beneficial features of AC derived from SS comprise the comparatively large surface area, porosity, enriched surface functional groups and presence of a high amount of metal species that can improve the catalytic activity. Hence, a sludge-based AC catalyst was fabricated in a single-step pyrolysis reaction with NaOH as the activation agent and was compared with HZSM5 zeolite in this study. The thermal decomposition and kinetics were invested via thermogravimetric analysis (TGA) for guidance and control of pyrolysis and catalytic pyrolysis and the design of the pyrolysis setup. The results indicated that the pyrolysis and catalytic pyrolysis contain four obvious stages and the main decomposition reaction occurred in the range of 200-600 °C. Coats-Redfern method was applied in the 2nd and 3rd devolatilization stages to estimate the reaction order and activation energy (E) from the mass loss data. The average activation energy (Em) values for the reaction orders n = 1, 2 and 3 were in the range of 6.67-20.37 kJ/mol for SS; 1.51-6.87 kJ/mol for HZSM5; and 2.29-9.17 kJ/mol for AC, respectively. According to the results, AC and HZSM5 both were able to improve the reaction rate of SS pyrolysis by abridging the Em value. Moreover, to generate and examine the effect of the catalysts on the quality of bio-oil, a fixed-bed pyrolysis system was designed and implemented. The composition analysis of the produced bio-oil was carried out via gas chromatography/mass spectrometry (GC/MS). The selected SS to catalyst ratios were 1:1, 2:1 and 4:1. The optimum ratio in terms of cracking the long-chain hydrocarbons and removing oxygen-containing compounds was 1:1 for both catalysts. The upgraded bio-oils with HZSM5 and AC were in the total range of C4-C17 with around 72% in the range of C4-C9. The bio-oil from pyrolysis of SS contained 49.27% oxygenated compounds while the presence of HZSM5 and AC dropped to 7.3% and 13.02%, respectively. Meanwhile, generation of value-added chemicals such as light aromatic compounds were significantly improved in the catalytic process. Furthermore, the fabricated AC catalyst was characterized by BET, SEM-EDX, FT-IR and TGA techniques. Overall, this research demonstrated that AC is an efficient catalyst in the pyrolysis of SS and can be used as a cost-competitive catalyst in contrast to HZSM5.

Keywords: Activated char, bio-oil, catalytic pyrolysis, HZSM5, sewage sludge.

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Authors: Tomas Makaras, Gintaras Svecevičius

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Landfill waste is a common problem as it has an economic and environmental impact even if it is closed. Landfill waste contains a high density of various persistent compounds such as heavy metals, organic and inorganic materials. As persistent compounds are slowly-degradable or even non-degradable in the environment, they often produce sublethal or even lethal effects on aquatic organisms. The aims of the present study were to estimate sublethal effects of the Kairiai landfill (WGS: 55°55‘46.74“, 23°23‘28.4“) leachate on the locomotor activity of rainbow trout Oncorhynchus mykiss juveniles using the original system package developed in our laboratory for automated monitoring, recording and analysis of aquatic organisms’ activity, and to determine patterns of fish behavioral response to sublethal effects of leachate. Four different concentrations of leachate were chosen: 0.125; 0.25; 0.5 and 1.0 mL/L (0.0025; 0.005; 0.01 and 0.002 as part of 96-hour LC50, respectively). Locomotor activity was measured after 5, 10 and 30 minutes of exposure during 1-minute test-periods of each fish (7 fish per treatment). The threshold-effect-concentration amounted to 0.18 mL/L (0.0036 parts of 96-hour LC50). This concentration was found to be even 2.8-fold lower than the concentration generally assumed to be “safe” for fish. At higher concentrations, the landfill leachate solution elicited behavioral response of test fish to sublethal levels of pollutants. The ability of the rainbow trout to detect and avoid contaminants occurred after 5 minutes of exposure. The intensity of locomotor activity reached a peak within 10 minutes, evidently decreasing after 30 minutes. This could be explained by the physiological and biochemical adaptation of fish to altered environmental conditions. It has been established that the locomotor activity of juvenile trout depends on leachate concentration and exposure duration. Modeling of these parameters showed that the activity of juveniles increased at higher leachate concentrations, but slightly decreased with the increasing exposure duration. Experiment results confirm that the behavior of rainbow trout juveniles is a sensitive and rapid biomarker that can be used in combination with the system for fish behavior monitoring, registration and analysis to determine sublethal concentrations of pollutants in ambient water. Further research should be focused on software improvement aimed to include more parameters of aquatic organisms’ behavior and to investigate the most rapid and appropriate behavioral responses in different species. In practice, this study could be the basis for the development and creation of biological early-warning systems (BEWS).

Keywords: Fish behavior biomarker, landfill leachate, locomotor activity, rainbow trout juveniles, sublethal effects.

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

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Authors: Y. Santosa, D. A. Rahman, C. Wulan, A. H. Mustari

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The global demand for long-tailed macaques for medical experimentation has continued to increase. Fulfillment of Indonesian export demands has been mostly from natural habitats, based on a harvesting quota. This quota has been determined according to the total catch for a given year, and not based on consideration of any demographic parameters or physical environmental factors with regard to the animal; hence threatening the sustainability of the various populations. It is therefore necessary to formulate a method for calculating a sustainable harvesting quota, based on population parameters in natural habitats. Considering the possibility of variations in habitat characteristics and population parameters, a time series observation of demographic and physical/biotic parameters, in various habitats, was performed on 13 groups of long-tailed macaques, distributed throughout the West Java, Lampung and Yogyakarta areas of Indonesia. These provinces were selected for comparison of the influence of human/tourism activities. Data on population parameters that was collected included data on life expectancy according to age class, numbers of individuals by sex and age class, and ‘ratio of infants to reproductive females’. The estimation of population growth was based on a population dynamic growth model: the Leslie matrix. The harvesting quota was calculated as being the difference between the actual population size and the MVP (minimum viable population) for each sex and age class. Observation indicated that there were variations within group size (24–106 individuals), gender (sex) ratio (1:1 to 1:1.3), life expectancy value (0.30 to 0.93), and ‘ratio of infants to reproductive females’ (0.23 to 1.56). Results of subsequent calculations showed that sustainable harvesting quotas for each studied group of long-tailed macaques, ranged from 29 to 110 individuals. An estimation model of the MVP for each age class was formulated as Log Y = 0.315 + 0.884 Log Ni (number of individual on ith age class). This study also found that life expectancy for the juvenile age class was affected by the humidity under tree stands, and dietary plants’ density at sapling, pole and tree stages (equation: Y=2.296 – 1.535 RH + 0.002 Kpcg – 0.002 Ktg – 0.001 Kphn, R2 = 89.6% with a significance value of 0.001). By contrast, for the sub-adult-adult age class, life expectancy was significantly affected by slope (equation: Y=0.377 = 0.012 Kml, R2 = 50.4%, with significance level of 0.007). The infant-toreproductive- female ratio was affected by humidity under tree stands, and dietary plant density at sapling and pole stages (equation: Y = - 1.432 + 2.172 RH – 0.004 Kpcg + 0.003 Ktg, R2 = 82.0% with significance level of 0.001). This research confirmed the importance of population parameters in determining the minimum viable population, and that MVP varied according to habitat characteristics (especially food availability). It would be difficult therefore, to formulate a general mathematical equation model for determining a harvesting quota for the species as a whole.

Keywords: Harvesting, long-tailed macaque, population, quota.

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Authors: C. Silveira, A. Ascenso, J. Ferreira, A. I. Miranda, P. Tuccella, G. Curci

Abstract:

Poor air quality is one of the main environmental causes of premature deaths worldwide, and mainly in cities, where the majority of the population lives. It is a consequence of successive land cover (LC) and use changes, as a result of the intensification of human activities. Knowing these landscape modifications in a comprehensive spatiotemporal dimension is, therefore, essential for understanding variations in air pollutant concentrations. In this sense, the use of air quality models is very useful to simulate the physical and chemical processes that affect the dispersion and reaction of chemical species into the atmosphere. However, the modelling performance should always be evaluated since the resolution of the input datasets largely dictates the reliability of the air quality outcomes. Among these data, the updated LC is an important parameter to be considered in atmospheric models, since it takes into account the Earth’s surface changes due to natural and anthropic actions, and regulates the exchanges of fluxes (emissions, heat, moisture, etc.) between the soil and the air. This work aims to evaluate the performance of the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem), when different LC classifications are used as an input. The influence of two LC classifications was tested: i) the 24-classes USGS (United States Geological Survey) LC database included by default in the model, and the ii) CLC (Corine Land Cover) and specific high-resolution LC data for Portugal, reclassified according to the new USGS nomenclature (33-classes). Two distinct WRF-Chem simulations were carried out to assess the influence of the LC on air quality over Europe and Portugal, as a case study, for the year 2015, using the nesting technique over three simulation domains (25 km², 5 km² and 1 km² horizontal resolution). Based on the 33-classes LC approach, particular emphasis was attributed to Portugal, given the detail and higher LC spatial resolution (100 m x 100 m) than the CLC data (5000 m x 5000 m). As regards to the air quality, only the LC impacts on tropospheric ozone concentrations were evaluated, because ozone pollution episodes typically occur in Portugal, in particular during the spring/summer, and there are few research works relating to this pollutant with LC changes. The WRF-Chem results were validated by season and station typology using background measurements from the Portuguese air quality monitoring network. As expected, a better model performance was achieved in rural stations: moderate correlation (0.4 – 0.7), BIAS (10 – 21µg.m^-3) and RMSE (20 – 30 µg.m^-3), and where higher average ozone concentrations were estimated. Comparing both simulations, small differences grounded on the Leaf Area Index and air temperature values were found, although the high-resolution LC approach shows a slight enhancement in the model evaluation. This highlights the role of the LC on the exchange of atmospheric fluxes, and stresses the need to consider a high-resolution LC characterization combined with other detailed model inputs, such as the emission inventory, to improve air quality assessment.

Keywords: Land cover, tropospheric ozone, WRF-Chem, air quality assessment.

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