Search results for: chemolithotrophic bacterial species

Authors: Margareta Rahayuningsih, Siti Alimah, Novita Hermayani, Misbahul Munir

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Wreathed Hornbill (Rhycticeros undulatus) was a protected bird that we can found in Mount Ungaran. It is known that the bird have been breeding and nesting on the mountain. The objective of the research was to analysis the materials composition of the Wreathed Hornbill nest wall plaster. The study was carried out in Curug Lawe and Gunung Gentong, Mount Ungaran Central Java. Nest wall plaster samples were collected from nest cavities were used by hornbill but after they left from the nest. The nest tree species on Gunung Gentong was Syzygium antisepticum and Syzigium glabratum on Curug Lawe. Materials analysis used proximate analysis and have been done on Chemistry Laboratory of Semarang State University. The result of proximate analysis showed that the material composition of nest wall plaster such as water, proteins. lipid, carbohydrate, and ash between Curug Lawe and Gunung Gentong was different. Except Carbohidrate, the highest componen showed in the nest wall plaster on Gunung Gentong.

Keywords: Mount Ungaran, nest cover entrance, Rhyticeros undulatus, proximate analysis

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Authors: Stelvin Sebastian, Andriya Annie Tom, Joyalanna Babu, Merin Joshy

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Introduction: The worldwide increase in the use of antibiotics in poultry and livestock industry to treat and prevent bacterial diseases and as growth promoters in feeds has led to the problem of development of antibiotic resistance both in animals and human population. Aim: To study the pattern of antibiotic use and prevalence of multidrug-resistant Escherichia coli in poultry chickens in selected farms in Muvattupuzha and to compare the spread of multidrug-resistant bacteria from poultry environment to UTI patients. Methodology: Two farms from each of 6 localities in Muvattupuzha were selected. A questionnaire on the pattern of antibiotic use and various farming practices were surveyed from farms. From each farm, 60samples of fresh fecal matter, litter from inside, litter from the outside shed, agricultural soil and control soil were collected, and antimicrobial susceptibility testing of E. coli was done. Antibiogram of UTI patients was collected from the secondary care hospital included in the study, and those were compared with resistance patterns of poultry samples. Results: From survey response antibiotics such as ofloxacin, enrofloxacin, levofloxacin, ciprofloxacin, colistin, ceftriaxone, neomycin, cephalexin, and oxytetracycline were used for treatment and prevention of infections in poultry. 31of 48 samples (51.66%) showed E. coli growth. 7 of 15 antibiotics (46.6%) showed resistance. Ampicillin, amoxicillin, meropenem, tetracycline showed 100% resistance to all samples. Statistical analysis confirmed similar resistance pattern in the poultry environment and UTI patients for antibiotics such as ampicillin, amoxicillin, amikacin, and ofloxacin. Conclusion: E. coli were resistant not only to extended-spectrum beta-lactams but also to carbapenems, which may be disseminated to the environment where litter was used as manure. This may due to irrational use of antibiotics in chicken or from their use in poultry feed as growth promoters. The study concludes the presence of multidrug-resistant E.coli in poultry and its spread to environment and humans, which may cause potentially serious implications for human health.

Keywords: multidrug resistance, escherichia coli, urinary tract infection, poultry

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Authors: Ijaz Ahmad

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Weed competition is one of the major biotic constraints in wheat crop productivity. Avena fatua L. and Silybum marianum (L.) Gaertn. are among the worst weeds of wheat, greatly deteriorating wheat quality subsequently reducing its market value. In this connection, two-year experiments were conducted in 2018 & 2019. Different seeding rate wheat viz; 80, 100, 120 and 140 kg ha-1 and different weeds ratio (A. fatua: S. marianum ) sown at the rate 1:8, 2:7, 3:6, 4:5, 5:4, 6:3, 7:2, 8:1 and 0:0 respectively. The weeds ratio and wheat densities are indirectly proportional. However, the wheat seed at the rate of 140 kg ha-1 has minimal weeds interference. Yield losses were 17.5% at weeds density 1:8 while 7.2% at 8:1. However, in wheat density, the highest percent losses were computed on 80 kg ha-1 while the lowest was recorded on 140 kg ha-1. Since due to the large leaf canopy of S. marianum other species can't sustain their growth. Hence, it has been concluded that S. marianum is the hotspot that causes reduction to the yield-related parameters, followed by A. fatua and the other weeds. Due to the morphological mimicry of A. fatua with wheat crop during the vegetative growth stage, it cannot be easily distinguished. Therefore, managing A. fatua and S. marianum before seed setting is recommended for reducing the future weed problem. Based on current studies, it is suggested that sowing wheat seed at the rate of 140 kg ha-1 is recommended to better compete with all the field weeds.

Keywords: fat content, holly thistle, protein content, weed competition, wheat, wild oat

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Authors: Anna-Mari Kok, Carel B. Oosthuizen, Namrita Lall

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Tuberculosis (TB) is a disease caused by the bacterial pathogen Mycobacterium tuberculosis. It is associated with high mortality rates in both developing and developed countries. Many higher plants are found that are medicinally associated with tuberculosis infection. Plants belonging to thirteen families were selected, based on their traditional usage for tuberculosis and its associated symptoms. Eight plants showed the best antimycobacterial activities (MIC-value ≤ 500.0 µg/ml) against M. tuberculosis H37Rv. LS was found to have a minimum inhibitory concentration (MIC) of 125 µg/ml whereas, Tulbaghia violacea, Heteromorpha arborescens, Sutherlandia frutescens, Eucalyptus deglupta, and Plectranthus neochilus were found to have a MIC value of 250 µg/ml against M. tuberculosis H37Rv. Cytotoxicity values on U937 and HepG2 cells were obtained and the IC50 values ranged between 40 ±4.30 and > 400 µg/ml for the U937 cell line and 72.4 ±1.50 and > 400 µg/ml for the HepG2 cell line. Heteromorpha arborescens had the lowest IC50 value in both cell lines and therefore showed moderate levels of toxicity. Of the 19 samples that underwent the 2, 2- diphenyl- 1- picrylhydrazyl (DPPH) antioxidant assay, Eucalyptus deglupta and Melianthus major showed significant free radical scavenging activities with concentrations of 1.33 and 1.32 µg/ml respectively for the inhibition of DPPH. Hepatotoxicity induced by acetaminophen identified Searsia lancea with hepatoprotective activity of 59.37% at a ¼ IC50 concentration. Out of the 7 samples that were investigated for their immunomodulatory capabilities, Eucalyptus deglupta produced the most IL-12 with Sutherlandia frutescens also showing positive results for IL-12 production. In the present study, Eucalyptus deglupta showed the most promising results with good activity against M. tuberculosis with an MIC-value of 250 µg/ml. It also has potent antioxidant activity with an IC50 value of 1.33 µg/ml. This sample also stimulated high production of the cytokine, IL-12. Searsia lancea showed moderate antimycobacterial acticvity with an MIC-value of 500 µg/ml. The antioxidant potential also showed promising results with an IC50 value of 4.50 µg/ml. The hepatoprotective capability of Searsia lancea was 59.34% at a ¼ IC50 concentration. Another sample Sutherlandia frutescens showed effective antimycobacterial activity with an MIC-value of 250 µg/ml. It also stimulated production of IL-12 with 13.43 pg/ml produced. These three samples can be considered for further studies for the consideration as adjuvants for current tuberculosis treatment.

Keywords: adjuvant, hepatoprotection, immunomodulation, tuberculosis

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Authors: Abdul Hafeez, Shahid Adeel, Ayesha Hussain

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There are number of plants species in the universe which give the protections from different diseases and give colour for the foods and textiles. The environmental condition of the universe suggested toward the ecofriendly textiles. The aim of the paper is to analyze the influence of pre & post mordanting of alum on radiated cotton fabric with Gamma Radiation of different doses by using Ipomoea indica leaves extract. Alum used as mordant with the concentration of 2, 4, 6, 8 and 10% as pre and post mordanting to observe the effect of light and colour fastness of radiated cotton. 6% of alum concentration in pre mordanting gave good colour strength 117.82 with darker in shade toward the greenish tone and in post mordanting 6% concentration gave good colour strength 102.19. The lab values show that the colour is darker in tone and gave bluish effect. Further results showed that alum gave good light and rubbing fastness on gamma radiated cotton fabric.

Keywords: Ipomoea indica, gamma radiation, alum, light fastness

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Authors: G. Quiroga-Cubides, A. Díaz, M. Gómez

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The genus Azotobacter has been widely used as bio-fertilizer due to its significant effects on the stimulation and promotion of plant growth in various agricultural species of commercial interest. In order to obtain significantly viable cellular concentration, a scale-up strategy for a liquid fermentation process (SmF) with two strains of A. chroococcum (named Ac1 and Ac10) was validated and adjusted at laboratory and pilot scale. A batch fermentation process under previously defined conditions was carried out on a biorreactor Infors®, model Minifors of 3.5 L, which served as a baseline for this research. For the purpose of increasing process efficiency, the effect of the reduction of stirring speed was evaluated in combination with a fed-batch-type fermentation laboratory scale. To reproduce the efficiency parameters obtained, a scale-up strategy with geometric and fluid dynamic behavior similarities was evaluated. According to the analysis of variance, this scale-up strategy did not have significant effect on cellular concentration and in laboratory and pilot fermentations (Tukey, p > 0.05). Regarding air consumption, fermentation process at pilot scale showed a reduction of 23% versus the baseline. The percentage of reduction related to energy consumption reduction under laboratory and pilot scale conditions was 96.9% compared with baseline.

Keywords: Azotobacter chroococcum, scale-up, liquid fermentation, fed-batch process

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Authors: Rachel Fanelwa Ajayi, Anovuyo Jonnas, Emmanuel I. Iwuoha

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Tuberculosis (TB) is an infectious disease caused by the bacterium (Mycobacterium tuberculosis) which has a predilection for lung tissue due to its rich oxygen supply. The mycobacterial cell has a unique innate characteristic which allows it to resist human immune systems and drug treatments; hence, it is one of the most difficult of all bacterial infections to treat, let alone to cure. At the same time, multi-drug resistance TB (MDR-TB) caused by poorly managed TB treatment, is a growing problem and requires the administration of expensive and less effective second line drugs which take much longer treatment duration than fist line drugs. Therefore, to acknowledge the issues of patients falling ill as a result of inappropriate dosing of treatment and inadequate treatment administration, a device with a fast response time coupled with enhanced performance and increased sensitivity is essential. This study involved the synthesis of electroactive platforms for application in the development of nano-biosensors suitable for the appropriate dosing of clinically diagnosed patients by promptly quantifying the levels of the TB drug; Isonaizid. These nano-biosensors systems were developed on gold surfaces using the enzyme N-acetyletransferase 2 coupled to the cysteamine modified poly(8-anilino-1-napthalene sulphonic acid)/zinc oxide nanocomposites. The morphology of ZnO nanoparticles, PANSA/ZnO nano-composite and nano-biosensors platforms were characterized using High-Resolution Transmission Electron Microscopy (HRTEM) and High-Resolution Scanning Electron Microscopy (HRSEM). On the other hand, the elemental composition of the developed nanocomposites and nano-biosensors were studied using Fourier Transform Infra-Red Spectroscopy (FTIR) and Energy Dispersive X-Ray (EDX). The electrochemical studies showed an increase in electron conductivity for the PANSA/ZnO nanocomposite which was an indication that it was suitable as a platform towards biosensor development.

Keywords: N-acetyletransferase 2, isonaizid, tuberculosis, zinc oxide

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Authors: Nomakholwa F. Stokwe, Antoinette P. Malan

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Woolly apple aphid (WAA), Eriosoma lanigerum, is an important pest of apples worldwide. The aphid feeds above ground on buds and leaf axils and the roots of apple trees. Entomopathogenic nematodes (EPNs) of the two families, Steinernematidae and Heterorhabditidae, and their symbiotic bacteria have generated extensive interest as inundative applied biological control agents of insects. With the development of the resistance of WAA to chemicals, export restrictions, and the inability of parasitoids to control the aphid successfully early in the season, considering EPNs as an alternative biocontrol agent is important. Seven EPN species were tested for their pathogenicity against WAA. Laboratory bioassays identified S. yirgalemense and H. zealandica as being the most virulent against the subterranean stage of the WAA, with a mortality rate of 48% and 38%, respectively. Studies on the effect of WAA size showed that the last instar is most susceptible to infection, whereas smaller instars appear to be too small for nematode penetration and infection. Neither increasing the exposure period of the aphids nor increasing the nematode concentration affected the infection rate positively. The haemolymph of WAA showed an inhibitory effect on the development of the symbiotic bacteria, preventing the completion of the nematode’s life cycle.

Keywords: apples, biocontrol, entomopathogenic nematodes, woolly apple aphid

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Authors: Hassan Jebreen

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These models of a conservative pollutant in groundwater do not include representation of processes in soils and in the unsaturated zone, or biogeochemical processes in groundwater, These demonstration models can be used as the basis for more detailed simulations of the impacts of pollution sources at a local scale, but such studies should address processes related to specific pollutant species, and should consider local hydrogeology in more detail, particularly in relation to possible impacts on shallow systems which are likely to respond more quickly to changes in pollutant inputs. The results have demonstrated the interaction between groundwater flow fields and pollution sources in abstraction areas, and help to emphasise that wadi development is one of the key elements of water resources planning. The quality of groundwater in the Hebron area indicates a gradual increase in chloride and nitrate with time. Since the aquifers in Hebron districts are highly vulnerable due to their karstic nature, continued disposal of untreated domestic and industrial wastewater into the wadi will lead to unacceptably poor water quality in drinking water, which may ultimately require expensive treatment if significant health problems are to be avoided. Improvements are required in wastewater treatment at the municipal and domestic levels, the latter requiring increased public awareness of the issues, as well as improved understanding of the hydrogeological behaviour of the aquifers.

Keywords: groundwater, models, pollutants, wadis, hebron

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Authors: Francis Gbogbo, Angelica Ama Essandoh, Wendy Teresa Baffoe, Henry Groos, Charles Mario Boateng, Emmanuel Robert Blankson

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Baseline data on plastic landing by fishers and monitoring of this is important in evaluating the success of plastic waste management efforts. This study investigated plastic and fish landed by beach seine fishers in Ghana, together with the rate of plastic deposition on an adjoining beach. Plastic constituted 31.6% of the total catch, and 41.7% of the fish landed by weight. There were significant differences between the average weight of fish (139.58±53.6kg) and plastic (65.73±14.6kg) landed per fishing session and the catch per unit effort of fish (183.4±76.7 kg/day) and plastic (88.4±35.2 kg/day). The mean weight of plastic landed per fishing session was higher than the mean weight of each of the 26 species of fisheries. The rate of plastic deposition on the beach was 8.1±2.5 plastic items per m2 per tidal cycle or 0.35±0.11kg plastic per m2 per tidal cycle, with food packs and tableware dominating the deposited plastic. The results suggested that ongoing water sachets and plastic bottle recycling in Ghana are yielding results and calls for targeted efforts in plastic food packs and tableware management.

Keywords: fishig, landing, plastic waste, intertidal area, fishing effort

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Authors: Marina Arino Martin, John McEvoy, Eakalak Khan

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Endoxifen is an active metabolite responsible for the effectiveness of tamoxifen, a chemotherapeutic drug widely used for endocrine responsive breast cancer and chemo-preventive long-term treatment. Tamoxifen and endoxifen are not completely metabolized in human body and are actively excreted. As a result, they are released to the water environment via wastewater treatment plants (WWTPs). The presence of tamoxifen in the environment produces negative effects on aquatic lives due to its antiestrogenic activity. Because endoxifen is 30-100 times more potent than tamoxifen itself and also presents antiestrogenic activity, its presence in the water environment could result in even more toxic effects on aquatic lives compared to tamoxifen. Data on actual concentrations of endoxifen in the environment is limited due to recent discovery of endoxifen pharmaceutical activity. However, endoxifen has been detected in hospital and municipal wastewater effluents. The detection of endoxifen in wastewater effluents questions the treatment efficiency of WWTPs. Studies reporting information about endoxifen removal in WWTPs are also scarce. There was a study that used chlorination to eliminate endoxifen in wastewater. However, an inefficient degradation of endoxifen by chlorination and the production of hazardous disinfection by-products were observed. Therefore, there is a need to remove endoxifen from wastewater prior to chlorination in order to reduce the potential release of endoxifen into the environment and its possible effects. The aim of this research is to isolate and identify bacteria strain(s) capable of degrading endoxifen into less hazardous compound(s). For this purpose, bacteria strains from WWTPs were exposed to endoxifen as a sole carbon and nitrogen source for 40 days. Bacteria presenting positive growth were isolated and tested for endoxifen biodegradation. Endoxifen concentration and by-product formation were monitored. The Monod kinetic model was used to determine endoxifen biodegradation rate. Preliminary results of the study suggest that isolated bacteria from WWTPs are able to growth in presence of endoxifen as a sole carbon and nitrogen source. Ongoing work includes identification of these bacteria strains and by-product(s) of endoxifen biodegradation.

Keywords: biodegradation, bacterial degraders, endoxifen, wastewater

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Authors: B. S. Choudri

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Introduction: Climate change is a major threat to rural livelihoods and to food security in the developing world, including Oman. The aim of this study is to provide a basis for policymakers and researchers in order to understand the impacts of climate change on agriculture and developing adaptation strategies in Oman. Methodology: The data was collected from different agricultural areas across the country with the help of a questionnaire survey among farmers, discussion with community, and observations at the field level. Results: The analysis of data collected from different areas within the country shows a shift in the sowing period of major crops and increased temperatures over recent years. Farmer community is adopting through diversification of crops, use of heat-tolerant species, and improved measures of soil and water conservation. Agriculture has been the main livelihood for most of the farmer communities in rural areas in the country. Conclusions: In order to reduce the effects of climate change at the local and farmer communities, risk reduction would be important along with an in-depth analysis of the vulnerability. Therefore, capacity building of local farmers and providing them with scientific knowledge, mainstreaming adaptation into development activities would be essential with additional funding and subsidies.

Keywords: agriculture, climate change, vulnerability, adaptation

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Authors: Ashraf Fayz Bekhet Abaskron

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This research is done to create new compositions for designs, finding inspiration from watercolor artworks displayed in SuanSunandha Palace. The researcher made a study in the history of the landmark, its importance, the paintings in the Palace, the types and characteristics of the flowers painted, as well as the artistic elements and principles of designs that went into the paintings. The information obtained led to the creation of six totally new designs. The designs incorporated standard international designs and artistic principles and still kept to the original style of the watercolor paintings in SuanSunandha Palace. Following the paintings, the designs are divided into three categories: Orchids, Roses, and Flowers from literature. The researcher used the components of the flowers including rounded-petal flowers, wavy-edged petals, flowers with pointed petals, leaves, vines, and branches. All of them are represented in the original paintings. Upon the original, the researcher switched these elements and their proportions around to create a more modern design. The original forms are used as references since they contain the characteristics of each flower species. The work created achieved an updated trait and simultaneously reflects the charms and timeless beauty of the watercolor paintings displayed in SuanSunandha Palace, which still exists in today’s world.

Keywords: art, craft, design, Oman, weaving watercolor, painting, flower, Suan Sunandhagolden ratio, Fibonacci numbers, textile design, designs

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Authors: Pallabi Kalita, Hui Tag, Loxmi Jamoh, H. N. Sarma, A. K. Das

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Wild edible food plants contain a number of organic phytochemical that have been linked to the promotion of good health. These plants used by the local people of Arunachal Pradesh (Northeast India) are found to have high nutritional potential to maintain general balance diet. A study was conducted to evaluate the nutritional potential of five commonly found, unexplored wild food plants namely, Piper pedicellatum C. DC (leaves), Gonostegia hirta (Blume ex Hassk.) Miq. (leaves), Mussaenda roxburghii Hook. f. (leaves), Solanum spirale Roxb. (leaves and fruits) and Cyathea spinulosa Wall. ex Hook. (pith portion and tender rachis) from East Siang District of Arunachal Pradesh Northeast (India) for ascertaining their suitability for utilization as supplementary food. Results of study revealed that P. pedicellatum, C. spinulosa, and S. spirale (leaves) are the most promising species which have high nutritional content out of the five wild food plants investigated which is required for the normal growth and development of human.

Keywords: wild edible plants, gross energy, Gonostegia hirta, Cyathea spinulosa

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Authors: Adebayo Adewumi

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Emu Dromaius novaehollandiae the second largest bird in the world started its domestication in the United States in the early 1980's and the present trend in the production of emu in the U.S can be compared with cattle industry. As the population of many wildlife species in Nigeria declined due to unsustainable harvest of bush meat, animals like snails, antelopes,Ostrich, Emu and rodents have been domesticated. Although this improved livestock production in Nigeria, the basic physiological parameters of these mini- livestock are not known. Especially the intra-erythrocyte trace elements of domesticated emu, For this study, emu blood was obtained from Ajanla farms, Ibadan, Oyo State, Nigeria. There, 16 emus at age of 20 months were bled through jugular vein in a semi-intensive system for a period of 12 months. The intra-erythrocyte trace elements Cu, Zn, and Mg in healthy Emu were measured. The influences of sex and age on these parameters were investigated. No age or sex differences were observed in intra-erythrocytic Cu levels. Intra-erythrocytic Zn and Mg levels were significantly higher (P<0.05) in young Emu than in adults while males used significantly (P<0.05) higher intra erythrocytic Mg than females. intra-erythrocyte trace elements Cu, Zn and Mg is a good pointer to haemoglobin concentration which determines the state of wellness of an animal. The information from this work has provided a baseline data for further understanding of erythrocyte biochemistry of Emu in Nigeria.

Keywords: intra erythrocyte, trace elements, Emu, biochemistry

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Authors: O. O. Leigh, L. C. Agbugba, A. O. Oyewunmi, A. E. Ibiam, A. Hassan

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Accuracy of insemination timing is a key determinant of high pregnancy rates in livestock breeding stations. The estrous detector probes are a recent introduction into the Nigerian livestock farming sector. Many of these probes are species-labeled and they measure changes in the vaginal mucus resistivity (VMR) during the stages of the estrous cycle. With respect to size and shaft conformation, the Draminski® swine estrous detector probe (sEDP) is quite similar to the bovine estrous detector probe. We investigated the reliability of the sEDP at insemination time on two farms designated as FM A and FM B. Cows (Bunaji, n=20 per farm) were evaluated for VMR at 16th h post standard OvSynch protocol, with concurrent insemination on FM B only. The difference in the mean VMR between FM A (221 ± 24.36) Ohms and FM B (254 ± 35.59) Ohms was not significant (p > 0.05). Sixteen cows (80%) at FM B were later (day 70) confirmed pregnant via rectal palpation and calved at term. These findings suggest consistency in VMR evaluated with sEDP at insemination as well as a high predictability for VMR associated with good pregnancy rates in dairy cattle. We conclude that Draminski® swine estrous detector probe is reliable in determining time of insemination in cattle breeding stations.

Keywords: dairy cattle, insemination, swine estrous probe, vaginal mucus resistivity

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Ouafa Benaida, Abdelhamid Loukil, Adda Ali Pacha

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In recent years, the growing interest of scientists in the field of image processing and analysis of underwater images and videos has been strengthened following the emergence of new underwater exploration techniques, such as the emergence of autonomous underwater vehicles and the use of underwater image sensors facilitating the exploration of underwater mineral resources as well as the search for new species of aquatic life by biologists. Indeed, underwater images and videos have several defects and must be preprocessed before their analysis. Underwater landscapes are usually darkened due to the interaction of light with the marine environment: light is absorbed as it travels through deep waters depending on its wavelength. Additionally, light does not follow a linear direction but is scattered due to its interaction with microparticles in water, resulting in low contrast, low brightness, color distortion, and restricted visibility. The improvement of the underwater image is, therefore, more than necessary in order to facilitate its analysis. The research presented in this paper aims to implement and evaluate a set of classical techniques used in the field of improving the quality of underwater images in several color representation spaces. These methods have the particularity of being simple to implement and do not require prior knowledge of the physical model at the origin of the degradation.

Keywords: underwater image enhancement, histogram normalization, histogram equalization, contrast limited adaptive histogram equalization, single-scale retinex

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Authors: Kiran Fatima, Kashif Ali

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Staphylococcus aureus is an opportunistic human as well as animal pathogen that causes a variety of diseases. A total of 70 staphylococci isolates were obtained from soil, water, yogurt, and clinical samples. The likely staphylococci clinical isolates were identified phenotypically by different biochemical tests. Molecular identification was done by PCR using species-specific 16S rRNA primer pairs, and finally, 50 isolates were found to be positive as Staphylococcus aureus, sciuri, xylous and cohnii. Screened isolates were further analyzed by several microbiological diagnostics tests, including gram staining, coagulase, capsule, hemolysis, fermentation of glucose, lactose, maltose, and sucrose tests enzymatic reactions. It was found that 78%, 81%, and 51% of isolates were positive for gelatin hydrolysis, protease, and lipase activities, respectively. Antibiogram analysis of isolated Staphylococcus aureus strains with respect to different antimicrobial agents revealed resistance patterns ranging from 57 to 96%. Our study also shows 70% of strains to be MRSA, 54.3% as VRSA, and 54.3% as both MRSA and VRSA. All the identified isolates were subjected to detection of mecA, nuc, and hlb genes, and 70%, 84%, and 40% were found to harbour mecA, nuc, and hlb genes, respectively. The current investigation is highly important and informative for the high-level multidrug-resistant Staphylococcus aureus infections inclusive also of methicillin and vancomycin.

Keywords: MRSA, VRSA, mecA, MSSA

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Authors: Malith Premarathne, Shehan Bandara, Kaushalya G. Batawala, Thilini U. Ariyadasa

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The rapid depletion of fossil fuel supplies and the emission of carbon dioxide by their continued combustion have paved the way for increased production of carbon-neutral biodiesel from naturally occurring oil sources. The high biomass growth rate and lipid production of microalgae make it a viable source for biodiesel production compared to conventional feedstock. In Sri Lanka, the production of biodiesel by employing indigenous microalgae species is at its emerging stage. This work was an attempt to compare the various pre-treatment methods before extracting lipids such as autoclaving, microwaving and sonication. A mixed culture of microalgae predominantly consisting of Chlorella sp. was obtained from Beire Lake which is an algae rich, organically polluted water body located in Colombo, Sri Lanka. After each pre-treatment method, a standard solvent extraction using Bligh and Dyer’s method was used to compare the total lipid content in percentage dry weight (% dwt). The fatty acid profiles of the oils extracted with each pretreatment method were analyzed using gas chromatography-mass spectrometry (GC-MS). The properties of the biodiesels were predicted by Biodiesel Analyzer© Version 1.1, in order to compare with ASTM 6751-08 biodiesel standard.

Keywords: biodiesel, lipid extraction, microalgae, pre-treatment

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Authors: Slim Amami

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A model is developed to prevent the risks related to climate conditions in the agricultural sector. It will determine the yearly optimum premium to be paid by a farmer in order to reach his required turnover. The model is mainly based on both climatic stability and 'soft' responses of usually grown species to average climate variations at the same place and inside a safety ball which can be determined from past meteorological data. This allows the use of linear regression expression for dependence of production result in terms of driving meteorological parameters, main ones of which are daily average sunlight, rainfall and temperature. By a simple best parameter fit from the expert table drawn with professionals, optimal representation of yearly production is deduced from records of previous years, and yearly payback is evaluated from minimum yearly produced turnover. Optimal premium is then deduced, and gives the producer a useful bound for negotiating an offer by insurance companies to effectively protect their harvest. The application to wheat production in the French Oise department illustrates the reliability of the present model with as low as 6% difference between predicted and real data. The model can be adapted to almost every agricultural field by changing state parameters and calibrating their associated coefficients.

Keywords: agriculture, database, meteorological factors, production model, optimal price

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Authors: O. S. Pradeep, S. Vigneshwaran, K. Praveen Kumar, K. Jeyendran, V. R. Sanal Kumar

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The influence of injector attitude on wall heat flux plays an important role in predicting the start-up transient and also determining the combustion chamber wall durability of liquid rockets. In this paper comprehensive numerical studies have been carried out on an idealized liquid rocket combustion chamber to examine the transient wall heat flux during its start-up transient at different injector attitude. Numerical simulations have been carried out with the help of a validated 2d axisymmetric, double precision, pressure-based, transient, species transport, SST k-omega model with laminar finite rate model for governing turbulent-chemistry interaction for four cases with different jet intersection angles, viz., 0^o, 30^o, 45^o, and 60^o. We concluded that the jets intersection angle is having a bearing on the time and location of the maximum wall-heat flux zone of the liquid rocket combustion chamber during the start-up transient. We also concluded that the wall heat flux mapping in liquid rocket combustion chamber during the start-up transient is a meaningful objective for the chamber wall material selection and the lucrative design optimization of the combustion chamber for improving the payload capability of the rocket.  

Keywords: combustion chamber, injector, liquid rocket, rocket engine wall heat flux

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Authors: Adepeju Simon-Oke, Olatunji Odeyemi, Mobolanle Oniya

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Urinary tract infection has become the most common bacterial infections in humans, both at the community and hospital settings; it has been reported in all age groups and in both sexes. This study was carried out in order to determine and evaluate the prevalence, current drug susceptibility pattern of the isolated organisms and identify the associated risk factors of UTIs among the pregnant women in Akure, Ondo State, Nigeria. A cross-sectional study was conducted on the urine of pregnant women, and socio-demographic information of the women was collected. A total of 300 clean midstream urine samples were collected, and a general urine microscopic examination and culture were carried out, the Microbact identification system was used to identify gram-negative bacteria. Out of the 300 urine samples cultured, 183(61.0%) yielded significant growth of urinary pathogens while 117(39.0%) yielded either insignificant growth or no growth of any urinary pathogen. Prevalence of UTI was significantly associated with the type of toilet used, symptoms of UTI, and previous history of urinary tract infection (p<0.05). Escherichia coli 58(31.7%) was the dominant pathogen isolated, and the least isolated uropathogens were Citrobacter freudii and Providencia retgerri 2(1.1%) respectively. Gram-negative bacteria showed 77.6%, 67.9%, and 61.2% susceptibility to ciprofloxacin, augmentin, and chloramphenicol, respectively. Resistance against septrin, chloramphenicol, sparfloxacin, amoxicillin, augmentin, gentamycin, pefloxacin, trivid, and streptomycin was observed in the range of 23.1 to 70.1%. Gram-positive uropathogens isolated showed high resistance to amoxicillin (68.4%) and high susceptibility to the remaining nine antibiotics in the range 65.8% to 89.5%. This study justifies that pregnant women are at high risk of UTI. Therefore screening of pregnant women during antenatal clinics should be considered very important to avoid complications. Health education with regular antenatal and personal hygiene is recommended as precautionary measures to UTI.

Keywords: pregnant women, prevalence, risk factor, UTIs

Procedia PDF Downloads 133

Authors: Victoria Goodall, Paul Fatti, Norman Owen-Smith

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Hidden Markov Models have become popular for the analysis of animal tracking data. These models are being used to model the movements of a variety of species in many areas around the world. A common assumption of the model is that the observations need to have regular time steps. In many ecological studies, this will not be the case. The objective of the research is to modify the movement model to allow for irregularly spaced locations and investigate the effect on the inferences which can be made about the latent states. A modification of the likelihood function to allow for these irregular spaced locations is investigated, without using interpolation or averaging the movement rate. The suitability of the modification is investigated using GPS tracking data for lion (Panthera leo) in South Africa, with many observations obtained during the night, and few observations during the day. Many nocturnal predator tracking studies are set up in this way, to obtain many locations at night when the animal is most active and is difficult to observe. Few observations are obtained during the day, when the animal is expected to rest and is potentially easier to observe. Modifying the likelihood function allows the popular Hidden Markov Model framework to be used to model these irregular spaced locations, making use of all the observed data.

Keywords: hidden Markov Models, irregular observations, animal movement modelling, nocturnal predator

Procedia PDF Downloads 240

Authors: Silvana Caglieri

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Theoretical study of acetylation of p-methylaniline catalyzed by Cu2+ ions from the analysis of intermediate of the reaction was carried out. The study of acetylation of amines is of great interest by the utility of its products of reaction and is one of the most frequently used transformations in organic synthesis as it provides an efficient and inexpensive means for protecting amino groups in a multistep synthetic process. Acetylation of amine is a nucleophilic substitution reaction. This reaction can be catalyzed by Lewis acid, metallic ion. In reaction mechanism, the metallic ion formed a complex with the oxygen of the acetic anhydride carbonyl, facilitating the polarization of the same and the successive addition of amine at the position to form a tetrahedral intermediate, determining step of the rate of the reaction. Experimental work agreed that this reaction takes place with the formation of a tetrahedral intermediate. In the present theoretical work were investigated the structure and energy of the tetrahedral intermediate of the reaction catalyzed by Cu2+ ions. Geometries of all species involved in the acetylation were made and identified. All of the geometry optimizations were performed by the method at the DFT/B3LYP level of theory and the method MP2. Were adopted the 6-31+G* basis sets. Energies were calculated using the Mechanics-UFF method. Following the same procedure it was identified the geometric parameters and energy of reaction intermediate. The calculations show 61.35 kcal/mol of energy for the tetrahedral intermediate and the energy of activation for the reaction was 15.55 kcal/mol.

Keywords: amides, amines, DFT, MP2

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Authors: Fawad Ali, Muhammad Ateeq, Ikhtiar Khan

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Ground water, a major source of drinking water supply in Peshawar has been severely contaminated by leather tanning industry. Effluents from the tanneries contain high concentration of chromium besides several other chemical species. Release of untreated effluents from the tanning industry has severely damaged surface and ground water, agriculture soil as well as vegetables and crops. Chromium is a well-known carcinogenic and mutagenic agent. Once in the human food chain, it causes multiple problems to the exposed population including various types of cancer, skin dermatitis, and DNA damage. In order to assess the extent of chromium and other heavy metals contamination, water samples were analyzed for heavy metals using Graphite Furnace Atomic Absorption Spectrometer (GFAAS, Analyst 700, Perkin Elmer). Total concentration of chromium was above the permissible limit (0.048 mg/l) in 85% of the groundwater (drinking water) samples. The concentration of cobalt, manganese, cadmium, nickel, lead, zinc and iron was also determined in the ground water, surface water, agriculture soil, and vegetables samples from the affected area.

Keywords: heavy metals, soil, groundwater, tannery effluents, food chain

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Authors: Seyed Hassan Moosa-kazemi, Hassan Vatandoost

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Malaria, Dirofilaria immitis (dog heart worm), and D. repens (dirofilariasis), which are transmitted by mosquitoes, have been reported in Iran. The Iranian mosquito fauna includes seven genera, 65 species, and three subspecies. Aedes albopictus has been reported since. West Nile, Sindbis, Dengue, Japanese encephalitis viruses, and the nematode Setaria (setariasis) has been reported in the country but there are no information about their vectors in Iran. Iran is malaria elimination phase. Insecticides residual spraying (IRS), distributed of insecticides long lasting treated nets (ITNs), fogging, release of larvivours fishes and Bacillus thuringiensis, chemical larviciding, as well as case finding and manipulation and modification of breeding places carried out thought the IVM program in the country. Prolonged exposure to insecticides over several generations of the vectors, develop resistance, a capacity to survive contact with insecticides. However, use of insecticides in agriculture has often been implicated as contributing to resistance in mosquito’s vectors. Resistance of mosquitoes to some insecticides has been documented just within a few years after the insecticides were introduced. Some enzymes such as monooxygenases, esterases and glutathione S-transferases have been considered as a reason for resistance to pyrethroid insecticides. In conclusion, regarding to documented resistance and tolerance of mosquitoes vectors to some insecticides, resistance management is suggested by using new insecticide with novel mode of action.

Keywords: control, Iran, resistance, vector

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Authors: Jing Ren, Guifeng Han

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The mental health of most college students in China is negative due to the multiple pressures of academics, life, and employment. The problem of psychological stress has been widely discussed and needs to be resolved immediately. Therefore, six typical green spaces in Chongqing University, China, were selected to explore the relationship between eight environmental characteristics and students' stress relief. A path analysis model is established using Amos26.0 to explain the paths for environmental characteristics influencing psychological stress relief. The results show that (1) tree species diversity (TSD) has a positive effect on stress relief, thus green coverage ratio (GCR), the proportion of water area (WAP), visual green index (VGI), and color richness (CR) have both positive and negative effects; (2) CR could reduce stress directly and indirectly, while GCR, TSD, WAP, and VGI could only reduce stress indirectly, and the most effective path is TSD→extent→stress relief; (3) CR can reduce stress more greatly for males than females, CR and VGI have better effects for art students than science students. The study can provide a theoretical reference for planning and designing campus living environments to improve students' mental health.

Keywords: public health, residential environment, space planning and management, mental health, path analysis

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Authors: Islam Nowisser, Noha Farag, Mohamed El Azizi

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Helicobacter pylori is a highly important human pathogen which inhabits about 50% of the population worldwide. Infection with this bacteria is very hard to treat, with high probability of recurrence. H. pylori causes severe gastric diseases, including peptic ulcer, gastritis, and gastric cancer, which has been linked to chronic inflammation. The infection has been reported to be associated with high levels of pro-inflammatory cytokines, especially IL-1β and TNF-α. The aim of the current study is to investigate the molecular mechanisms by which H. pylori activates NLRP3 inflammasome and its contribution to Il-1 β production in an innate cellular model. H. pylori PMSS1 and G27 standard strains, as well as the PMSS1 isogenic mutant strain PMSS1ΔVacA and G27ΔVacA, G27ΔCagA in addition to clinical isolates obtained from biopsy samples from the antrum and corpus mucosa of chronic gastritis patients, were used to establish infection in RAW-264.7 macrophages. The production levels of TNF-α and IL-1β was assessed using ELISA. Since expression of these cytokines is often regulated by the transcription factor complex, nuclear factor-kB (NF-kB), the activation of NF-κB in H. pylori infected cells was also evaluated by luciferase assay. Genomic DNA was extracted from bacterial cultures of H. pylori clinical isolates as well as the standard strains and their corresponding mutants, where they were evaluated for the cagA pathogenicity island and vacA expression. The correlation between these findings and expression of the cagA Pathogenicity Island and vacA in the bacteria was also investigated. The results showed IL-1β, and TNF-α production significantly increased in raw macrophages following H. pylori infection. The cagA+ and vacA+ H. pylori strains induced significant production of IL-1β compared to cagA- and vacA- strains. The activation pattern of NF-κB was correlated in the isolates to their cagA and vacA expression profiles. A similar finding could not be confirmed for TNF-α production. Our study shows the ability of H. pylori to activate NF-kB and induce significant IL-1β production as a possible mechanism for the augmented inflammatory response seen in subjects infected with cagA+ and vacA+ H. pylori strains that would lead to the progression to more severe form of the disease.

Keywords: Helicobacter pylori, IL-1β, inflammatory cytokines, nuclear factor KB, TNF-α

Procedia PDF Downloads 118