Search results for: biological ontology

Authors: Siddharth Satishchandran, Brian Khumalo

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Humans are able to derive semantic content from syntactic and pragmatic sources. Multimodal evidence from signaling theory, which examines communication between individuals within and across species, suggests that non-human primates possess similar syntactic and pragmatic capabilities. However, the extent remains unknown because primate pragmatics are relatively under-examined. Our paper reviews research within communication theory amongst non-human primates to understand current theoretical trends. We examine evidence for primate pragmatic capacities through observational, experimental, and theoretical work on gestures. Given fragmented theoretical perspectives, we provide a unified framework of communication for future research that contextualizes the available research under code biology. To achieve this, we rely on biological semiotics (biosemiotics), the philosophy of biology investigating prelinguistic meaning-making as a function of signs and codes. We close by discussing areas of potential research for studying gestural pragmatics amongst non-human primates, particularly chimpanzees (Pan troglodytes), Diana monkeys (Cercopithecus diana), and other potential candidates.

Keywords: pragmatics, non-human primates, gestural communication, biological semiotics

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Authors: Mónica P. Cala, Juan S. Carreño, Roland J.W. Meesters

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Recently, collection of biological fluids on special filter papers has become a popular micro-sampling technique. Especially, the dried blood spot (DBS) micro-sampling technique has gained much attention and is momently applied in various life sciences reserach areas. As a result of this popularity, DBS are not only intensively competing with the venous blood sampling method but are at this moment widely applied in numerous bioanalytical assays. In particular, in the screening of inherited metabolic diseases, pharmacokinetic modeling and in therapeutic drug monitoring. Recently, microsampling techniques were also introduced in “omics” areas, whereunder metabolomics. For a metabolic profiling study we applied micro-sampling of biological fluids (blood and plasma) from healthy controls and from women with breast cancer. From blood samples, dried blood and plasma samples were prepared by spotting 8uL sample onto pre-cutted 5-mm paper disks followed by drying of the disks for 100 minutes. Dried disks were then extracted by 100 uL of methanol. From liquid blood and plasma samples 40 uL were deproteinized with methanol followed by centrifugation and collection of supernatants. Supernatants and extracts were evaporated until dryness by nitrogen gas and residues derivated by O-methyxyamine and MSTFA. As internal standard C17:0-methylester in heptane (10 ppm) was used. Deconvolution and alignment of and full scan (m/z 50-500) MS data were done by AMDIS and SpectConnect (http://spectconnect.mit.edu) software, respectively. Statistical Data analysis was done by Principal Component Analysis (PCA) using R software. The results obtained from our preliminary study indicate that the use of dried blood/plasma on paper disks could be a powerful new tool in metabolic profiling. Many of the metabolites observed in plasma (liquid/dried) were also positively identified in whole blood samples (liquid/dried). Whole blood could be a potential substitute matrix for plasma in Metabolomic profiling studies as well also micro-sampling techniques for the collection of samples in clinical studies. It was concluded that the separation of the different sample methodologies (liquid vs. dried) as observed by PCA was due to different sample treatment protocols applied. More experiments need to be done to confirm obtained observations as well also a more rigorous validation .of these micro-sampling techniques is needed. The novelty of our approach can be found in the application of different biological fluid micro-sampling techniques for metabolic profiling.

Keywords: biofluids, breast cancer, metabolic profiling, micro-sampling

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Authors: Armando Cuspinera

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Humans are nature itself, being with non-human species part of the same ecosystem, but the praxis reflects that not all relations are the same. In fields of design such as Biomimicry, Biodesign, and Biophilic design exist different approaches towards nature, nevertheless, anthropocentric principles such as domination, objectivization, or exploitation are defined in the same as ecocentric principles of inherent importance in life itself. Anthropocentrism has showed humanity with pollution of the earth, water, air, and the destruction of whole ecosystems from monocultures and rampant production of useless objects that life cannot outstand this unaware rhythm of life focused only for the human benefits. Even if by nature the biosphere is resilient, studies showed in the Paris Agreement explain that humanity will perish in an unconscious way of praxis. This is why is important to develop a differentiation between anthropocentric and ecocentricprinciples in the praxis of design, in order to enhance respect, valorization, and positive affectivity towards other life forms is necessary to analyze what principles are reproduced from each practice of design. It is only from the study of immaterial dimensions of design such as symbolism, epistemology, and ontology that the relation towards nature can be redesigned, and in order to do so, it must be studies from the dimensions of ontological design what principles –anthropocentric or ecocentric- through what the objects enhance or focus the perception humans have to its surrounding. The things we design also design us is the principle of ontological design, and in order to develop a way of ecological design in which is possible to consider other species as users, designers or collaborators is important to extend the studies and relation to other living forms from a transdisciplinary perspective of techniques, knowledge, practice, and disciplines in general. Materials, technologies, and any kind of knowledge have the principle of a tool: is not good nor bad, but is in the way of using it the possibilities that exist within them. The collaboration of disciplines and fields of study gives the opportunity to connect principles from other cultures such as Deep Ecology and Environmental Humanities in the development of methodologies of design that study nature, integrates their strategies to our own species, and considers life of other species as important as human life, and is only form the studies of ontological design that material and immaterial dimensions can be analyzed and imbued with structures that already exist in other fields.

Keywords: design, antropocentrism, ecocentrism, ontological design

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Authors: Akın Kuyulu, Hanife Genç

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In present study, it was aimed to evaluate the gamma radiation impacts on tomato leaf miner at different biological stages. The laboratory colony of tomato leaf miner was used to set up the experiments. Different biological stages of the insects (eggs, 4^th instars and pupae) were irradiated using Cobalt-60 at doses of 0 (control), 100 Gray (Gy), 200 Gy, 300 Gy and 400 Gy in Cos-44HH-N source, at dose rate of 480 Gy/h. After irradiation, the eggs were incubated until hatching; the mature larvae were reared to complete their developments. Adult emergences from irradiated pupae were also evaluated. The results showed that there were no egg hatching at all tested irradiation doses. Although, the pupal percentages of irradiated mature larvae were 54%, 15% and 8% at doses of 100 Gy, 200 Gy and 300 Gy respectively, there were no adult emergences from irradiated mature larvae. On the other hand, the adult emergences were observed from irradiated pupae, decreased as radiation doses increased along with malformed adult appearance. Male and female individuals were out crossed with laboratory reared adults. Fecundity was correlated with radiation doses.

Keywords: irradiation, tomato, tomato leafminer, Tuta absoluta

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Authors: Indraj Singh, Xuan Lee, Yu-Chieh Cheng

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Scientists are very keen on biomimetic research that mimics biological species to micro-robotic devices with the novel functionalities and accessibility. The source of inspiration is the complexity, sophistication, and intelligence of the biological systems. In this work, we design a light-driven star-shaped microgripper, an autonomous soft device which can change the shape under the external stimulus such as light. The design is based on light-responsive Liquid Crystal Elastomers which fabricated onto the polymer coated aligned substrate. The change in shape, controlled by the anisotropicity and the molecular orientation of the Liquid Crystal Elastomer, based on the external stimulus. This artificial star-shaped microgripper is capable of autonomous closure and capable to grab the objects in response to an external stimulus. This external stimulus-responsive materials design, based on soft active smart materials, provides a new approach to autonomous, self-regulating optical systems.

Keywords: liquid crystal elastomers, microgripper, smart materials, robotics

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Authors: Amin Mojiri, Hamidi Abdul Aziz

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Leachate is created while water penetrates through the waste in a landfill, carrying some forms of pollutants. In literature, for treatment of wastewater and leachate, different ways of biological treatment were used. Sequencing batch reactor (SBR) is a kind of biological treatment. This study investigated the co-treatment of landfill leachate and domestic waste water by SBR and powdered activated carbon augmented (PAC) SBR process. The response surface methodology (RSM) and central composite design (CCD) were employed. The independent variables were aeration rate (L/min), contact time (h), and the ratio of leachate to wastewater mixture (%; v/v)). To perform an adequate analysis of the aerobic process, three dependent parameters, i.e. COD, color, and ammonia-nitrogen (NH3-N or NH4-N) were measured as responses. The findings of the study indicated that the PAC-SBR showed a higher performance in elimination of certain pollutants, in comparison with SBR. With the optimal conditions of aeration rate (0.6 L/min), leachate to waste water ratio (20%), and contact time (10.8 h) for the PAC-SBR, the removal efficiencies for color, NH3-N, and COD were 72.8%, 98.5%, and 65.2%, respectively.

Keywords: co-treatment, landfill Leachate, wastewater, sequencing batch reactor, activate carbon

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Authors: Sh. Najari Moghadam, M. Qomi, F. Raofie, J. Khadiv

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In this study, a liquid phase microextraction by hollow fiber (HF-LPME) combined with high performance liquid chromatography-UV detector was applied to preconcentrate and determine trace levels of Cyproheptadine in human urine and plasma samples. Cyproheptadine was extracted from 10 mL alkaline aqueous solution (pH: 9.81) into an organic solvent (n-octnol) which was immobilized in the wall pores of a hollow fiber. Then, it was back-extracted into an acidified aqueous solution (pH: 2.59) located inside the lumen of the hollow fiber. This method is simple, efficient and cost-effective. It is based on pH gradient and differences between two aqueous phases. In order to optimize the HF-LPME, some affecting parameters including the pH of donor and acceptor phases, the type of organic solvent, ionic strength, stirring rate, extraction time and temperature were studied and optimized. Under optimal conditions enrichment factor, limit of detection (LOD) and relative standard deviation (RSD(%), n=3) were up to 112, 15 μg.L−1 and 2.7, respectively.

Keywords: biological samples, cyproheptadine, hollow fiber, liquid phase microextraction

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Authors: Sarra Kitanou

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Water recycling and reuse is an effective measure to solve the water stress problem. The sustainable use of water resource has become a national development strategy in Morocco. A key aspect of improving overall sustainability is the potential for direct wastewater effluent reuse. However, the hybrid technology membrane bioreactors (MBR) have been identified as an attractive option for producing high quality and nutrient-rich effluents for wastewater treatment. It is based on complex interactions between biological processes, filtration process and rheological properties of the liquid to be treated. Currently, with the evolution of wastewater treatment projects in Morocco, the MBR technology can be used as a technology treating different types of wastewaters and to produce effluent with suitable quality for reuse. However, the energetic consumption of this process is a great concern, which can limit the development and implementation of this technology. In this investigation, the electric energy consumption of an ultrafiltration membrane bioreactor process in domestic wastewater treatment is evaluated and compared to some MBR installations based on literature review. Energy requirements of the MBR are linked to operational parameters and reactor performance. The analysis of energy consumption shows that the biological aeration and membrane filtration are more energy consuming than the other components listed as feed and recirculation pumps. Biological aeration needs 53% of the overall energetic consumption and the specific energy consumption for membrane filtration is about 25%. However, aeration is a major energy consumer, often exceeding 50% share of total energy consumption. The optimal results obtained on the MBR process (pressure p = 1.15 bar), hydraulic retention time (15 h) showed removal efficiencies up to 90% in terms of organic compounds removal, 100% in terms of suspended solids presence and up to 80% reduction of total nitrogen and total phosphorus. The effluent from this MBR system could be considered as qualified for irrigation reuse, showing its potential application in the future.

Keywords: hybrid process, membrane bioreactor, wastewater treatment, reuse

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Authors: F. Lops, G. Disciglio, A. Carlucci, G. Gatta, L. Frabboni, A. Tarantino, E. Tarantino

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Phelipanche ramosa L. Pomel is a root holoparasitic weed plant of many cultivations, particularly of tomato (Lycopersicum esculentum L.) crop. In Italy, Phelipanche problem is increasing, both in density and in acreage. The biological control of this parasitic weed involves the use of living organisms as numerous fungi and bacteria that can infect the parasitic weed, while it may improve the crop growth. This paper deals with the biocontrol with microorganism, including Arbuscular mycorrhizal (AM) fungi and fungal pathogens as Fusarium oxisporum spp. Colonization of crop roots by AM fungi can provide protection of crops against parasitic weeds because of a reduction in their seed germination and attachment, while F. oxisporum, isolated from diseased broomrape tubercles, proved to be highly virulent on P. ramosa. The experimental trial was carried out in open field at Foggia province (Apulia Region, Southern Italy), during the spring-summer season 2016, in order to evaluate the effect of four biological treatments: AM fungi and Fusarium oxisporum applied in the soil alone or combined together, and Rizosum Max^® product, compared with the untreated control, to reduce the P. ramosa infestation in processing tomato crop. The principal results to be drawn from this study under field condition, in contrast of those reported previously under laboratory and greenhouse conditions, show that both AM fungi and F. oxisporum do not provide the reduction of the number of emerged shoots of P. ramosa. This can arise probably from the low efficacy seedling of the agent pathogens for the control of this parasite in the field. On the contrary, the Rizosum Max^® product, containing AM fungi and some rizophere bacteria combined with several minerals and organic substances, appears to be most effective for the reduction of P. ramosa infestation.

Keywords: Arbuscular mycorrhized fungi, biocontrol methods, Phelipanche ramosa, tomato crop

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Authors: Achitphol Chookaew, Paramee Thongsukhsai, Patamarerk Engsontia, Narongwit Nakwan, Pritsana Raugrut

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Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.

Keywords: differentially expressed genes, early and late-stages, gene ontology, non-small cell lung cancer transcriptomics

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Authors: Mathias Twizeyimana, Urmila Adhikari, Julius P. Sserumaga, David Ingham

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The management of aflatoxins (naturally occurring toxins produced by certain fungi, most importantly Aspergillus flavus and A. parasiticus) relies mostly on the use of best cultural practices and, in some cases, the use of the biological control consisting of atoxigenic strains inhibiting the toxigenic strains through competition resulting in considerable toxin reduction. At AgBiome, we have built a core collection of over 100,000 fully sequenced microbes from diverse environments and employ both the microbes and their sequences in the discovery of new biological products for disease and pest control. The most common approach to finding beneficial microbes consists of isolating microorganisms from samples collected from diverse environments, selecting antagonistic strains through empirical screening, studying modes of action, and stabilization through the formulation of selected microbial isolates. A total of 608 diverse bacterial strains were screened using a high-throughput assay (48-well assay) to identify strains that inhibit toxigenic A. flavus growth on maize kernels. Active strains in 48-well assay had their pathogen inhibiting activity confirmed using the Flask Assay and were concurrently tested for their ability to reduce the aflatoxin content in maize grains. Strains with best growth inhibition and reduction of aflatoxin were tested in the greenhouse and field trials. From the field trials, three bacterial strains, AFS000009 (Pseudomonas chlororaphis), AFS032321 (Bacillus subtilis), AFS024683 (Bacillus velezensis), had aflatoxin concentrations (ppb) values that were significantly lower than those of inoculated control. The identification of biological products with high efficacy in inhibiting pathogen growth and eventually reducing the aflatoxin content will provide a valuable alternative to control strategies used in aflatoxin contamination management.

Keywords: aflatoxin, microorganism bacteria, biocontrol, beneficial microbes

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Authors: Dessy Laksyana Utami

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The sick building syndrome comprises of various nonspecific symptoms that occur in the occupants of a building. It is commonly increases sickness absenteeism and causes a decrease in productivity of the workers. Evidence suggests that what is called the Sick Building Syndrome are at least three separate entities, which has at least one cause. The following are some of the factors that might be primarily responsible for Sick Building Syndrome such as: Chemical contaminants, Biological contaminants, Inadequate ventilation and Electromagnetic radiation. In many cases it is due to insufficient maintenance of the HVAC (heating, ventilation, air conditioning) system in the building. As this syndrome is increasingly becoming a major occupational hazard. It was used the analytic cross-sectional design. Based on data obtained 80% of respondents reported significant ongoing health problems in the eyes, head, and the nose. 60% had bad symptoms in the throat, the stomach and cough, 50% had gastrointestinal disorders, 40% fatigue and 25% occurred all symptoms sick building syndrome. The 40 respondents were recruited to the study, with a mean age of 35 years (range 20-55). To support the evidence of Sick Building Syndrome, further checks are needed for some of the factors in next research, i.e. measurement of Chemical contaminants, Biological contaminants, inadequate ventilation & Electromagnetic radiation.

Keywords: indoor air pollution, sick building syndrome, indoor air quality, oil gas polution

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Authors: S. Cherif, A. Medjahed, M. Bouafia, A. Manallah

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A light wave is characterized by 4 characteristics: its amplitude, its frequency, its phase and the direction of polarization of its luminous vector (the electric field). It is in this last characteristic that we will be interested. The polarization of the light was introduced in order to describe the vectorial behavior of the light; it describes the way in which the electric field evolves in a point of space. Our work consists in studying diffusing mediums. Different types of biological fluids were selected to study the evolution of each with increasing scattering power of the medium, and in the same time to make a comparison between them. When crossing these mediums, the light undergoes modifications and/or deterioration of its initial state of polarization. This phenomenon is related to the properties of the medium, the idea is to compare the characteristics of the entering and outgoing light from the studied medium by a white light. The advantage of this model is that it is experimentally accessible workable intensity measurements with CCD sensors and allows operation in 2D. The latter information is used to discriminate some physical properties of the studied areas. We chose four types of milk to study the evolution of each with increasing scattering power of the medium.

Keywords: light polarization, Mueller matrix, Mueller images, diffusing medium, milk

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Authors: Rita Emília Szabó, Róbert Polanek, Tünde Tőkés, Zoltán Szabó, Szabolcs Czifrus, Katalin Hideghéty

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Purpose: Several feature of zebrafish are making them amenable for investigation on therapeutic approaches such as ionizing radiation. The establishment of zebrafish model for comprehensive radiobiological research stands in the focus of our investigation, comparing the radiation effect curves of neutron and photon irradiation. Our final aim is to develop an appropriate vertebrate model in order to investigate the relative biological effectiveness of laser driven ionizing radiation. Methods and Materials: After careful dosimetry series of viable zebrafish embryos were exposed to a single fraction whole-body neutron-irradiation (1,25; 1,875; 2; 2,5 Gy) at the research reactor of the Technical University of Budapest and to conventional 6 MeV photon beam at 24 hour post-fertilization (hpf). The survival and morphologic abnormalities (pericardial edema, spine curvature) of each embryo were assessed for each experiment at 24-hour intervals from the point of fertilization up to 168 hpf (defining the dose lethal for 50% (LD50)). Results: In the zebrafish embryo model LD50 at 20 Gy dose level was defined and the same lethality were found at 2 Gy dose from the reactor neutron beam resulting RBE of 10. Dose-dependent organ perturbations were detected on macroscopic (shortening of the body length, spine curvature, microcephaly, micro-ophthalmia, micrognathia, pericardial edema, and inhibition of yolk sac resorption) and microscopic (marked cellular changes in skin, cardiac, gastrointestinal system) with the same magnitude of dose difference. Conclusion: In our observations, we found that zebrafish embryo model can be used for investigating the effects of different type of ionizing radiation and this system proved to be highly efficient vertebrate model for preclinical examinations.

Keywords: ionizing radiation, LD50, relative biological effectiveness, zebrafish embryo

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Authors: Srinivasarao Kondaparla, Utsab Debnath, Awakash Soni, Vasantha Rao Dola, Manish Sinha, Kumkum Kumkum Srivastava, Sunil K. Puri, Seturam B. Katti

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In a focused exploration, we have designed synthesized and biologically evaluated chiral conjugated new chloroquine (CQ) analogs with substituted piperazines as antimalarial agents. In vitro as well as in vivo studies revealed that compound 7c showed potent activity [for in vitro IC₅₀= 56.98nM (3D7), 97.76nM (K1); for in vivo (up to at the dose of 12.5 mg/kg); SI = 3510] as a new lead of antimalarial agent. Other compounds 6b, 6d, 7d, 7h, 8c, 8d, 9a, and 9c are also showing moderate activity against CQ-sensitive (3D7) strain and superior activity against resistant (K1) strain of P. falciparum. Furthermore, we have carried out docking and 3D-QSAR studies of all in-house data sets (168 molecules) of chiral CQ analogs to explain the structure activity relationships (SAR). Our new findings specified the significance of H-bond interaction with the side chain of heme for biological activity. In addition, the 3D-QSAR study against 3D7 strain indicated the favorable and unfavorable sites of CQ analogs for incorporating steric, hydrophobic and electropositive groups to improve the antimalarial activity.

Keywords: piperazines, CQ-sensitive strain-3D7, in-vitro and in-vivo assay, docking, 3D-QSAR

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Authors: Mansouri Ouarda, Adbdennour Cherif, Boukarma Ziad

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Environmental and biological monitoring are used for the evaluation of exposure to industrial chemicals, and provide a tool for assessing workers’ exposure to chemicals. The organs or tissues where the first biological effects can be observed with increasing amounts of lead toxicity. This study aims at evaluating the effect of the metal element-trace; lead, on the sex hormones in male workers, exposed to this metal on the level of the manufacturing plant of lead accumulators. The results indicate a significant reduction of the testosterone concentration in exposed workers compared to the control. However, the rate of LH was strongly increased at the individuals exposed to Pb. A significant difference concerning the rate of FSH, the hormone Prolactin and cortisol was recorded. The indicators of the lead poisoning indicate a very highly significant increase in the value of Pbs which vary between (142-796 µg/L) among which 50% of the workers present a high lead poisoning and the value of PPZ which vary between (43-554µg/L). The biochemical parameters show a significant increase in the rate of the créatinine, the urea and the acid urique. The hepatic results show no significant differentiation in the rate of TGO and TGP between both groups of study. However the rates of the enzyme phosphatase alkaline, triglyceride, and cholesterol a significant difference were registered.

Keywords: hormons, parameters, physilogical, Pbs, PPZ

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Authors: C. Mekala, Indumathi M. Nambi

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Nitrogen pollution in groundwater arising from wastewater and fertilizer application through vadose zone is a major problem and it causes a prime risk to groundwater based drinking water supplies. Nitrogenous compounds namely ammonium, nitrate and nitrite fate and transport in soil subsurface were studied experimentally. The major process like sorption, leaching, biotransformation involving microbial growth kinetics, and biological clogging due to biomass growth were assessed and modeled with advection-dispersion reaction equations for ammonium, nitrate and acetate in a saturated, heterogeneous soil medium. The transport process was coupled with freundlich sorption and monod inhibition kinetics for immobile bacteria and permeability reduction due to biomass growth will be verified and validated with the numerical model. This proposed mathematical model will be very helpful in the development of a management model for a sustainable and safe wastewater reuse strategies such as irrigation and groundwater recharge.

Keywords: nitrogen species transport, transformation, biological clogging, biokinetic parameters, contaminant transport model, saturated soil

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Authors: Young Min Kim, Deokyeong Choe, Chul Soo Shin

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Monascus pigments, commonly used as a natural colorant in Asia, have many biological activities, such as cholesterol level control, anti-obesity, anti-cancer, and anti-oxidant, that have recently been elucidated. Especially, amino acid derivatives of Monascus pigments are receiving much attention because they have higher biological activities than original Monascus pigments. Previously, there have been two ways to produce amino acid derivatives: one-step production and two-step production. However, the one-step production has low purity, and the two-step production—precursor(orange pigments) fermentation and derivatives synthesis—has low productivity and growth rate during its precursor fermentation step. In this study, it was verified that pH is a key factor that affects the stability of orange pigments and the growth rate of Monascus. With an optimal pH profile obtained by pH-stat fermentation, we designed a process of precursor(orange pigments) fermentation that is a pH-controlled fed-batch fermentation. The final concentration of orange pigments in this process increased to 5.5g/L which is about 30% higher than the concentration produced from the previously used precursor fermentation step.

Keywords: cultivation process, fed-batch fermentation, monascus pigments, pH stability

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Iram Batool, Aamer Saeed, Irfan Zia Qureshi, Ayesha Razzaq, Saima Kalsoom

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Heterocyclic compounds analogues and their derivatives have attracted strong interest in medicinal chemistry due to their biological and pharmacological properties. A series of new thiazolopyrimidine carboxylates were conveniently synthesized by one-pot three-component reaction of ethyl acetoacetate, 2-aminothiazole and benzaldehyde substituted with electron-donating and electron-withdrawing groups in order to find some more potent antidiabetic and antibacterial drugs. The structures of synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopy. An in vitro antidiabetic effect was evaluated in adult male BALB/c mice and antibacterial activities were tested against Micrococcus luteus, Salmonella typhimurium, Bacillus subtilis, Bordetella bronchiseptica and Escherichia coli. Some of the tested compounds proved to possess good to excellent activities more than the reference drugs. An in silico molecular docking was also performed on synthesized compounds. The current study is expected to provide useful insights into the design of antidiabetic and antibacterial drugs and understanding the mechanism by which such drugs interact with RNA and diabetes target and exert their biochemical action.

Keywords: antidiabetic, antibacterial, MOE docking, thiazolopyrimidine

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Authors: Satya Eswari Jujjavarapu, Swasti Dhagat, Lata Upadhyay, Reecha Sahu

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Silver nanoparticles have a broad range of antimicrobial and antifungal properties ranging from soaps, pastes to sterilization and drug delivery systems. These can be synthesized by physical, chemical and biological methods; biological methods being the most popular owing to their non-toxic nature and reduced energy requirements. Microbial surfactants, produced on the microbial cell surface or excreted extracellularly are an alternative to synthetic surfactants for the production of silver nanoparticles. Hence, they are also called as green molecules. Microbial lipopeptide surfactants (biosurfactant) exhibit anti-tumor and anti-microbial properties and can be used as drug delivery agents. In this study, biosurfactant was synthesized by using a strain of acillus subtilis. The biosurfactant thus produced was analysed by emulsification assay, oil spilling test, and haemolytic test. Biosurfactant-mediated silver nanoparticles were synthesised by microwave irradiation of the culture supernatant and further characterized by UV–vis spectroscopy for a range of 400-600 nm. The UV–vis spectra showed a surface plasmon resonance vibration band at 410 nm corresponding to the peak of silver nanoparticles.

Keywords: biosurfactant, Bacillus subtilis, silver nano particle, lipopeptide

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Authors: Thandie Veronicah Sima, Moatlhodi Wiseman Letshwenyo

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Discharge of wastewater is one of the major sources of phosphorus entering streams, lakes and other water bodies causing undesired environmental problem such as eutrophication. This condition not only puts the ecosystem at risk but also causes severe economic damages. Stringent laws have been developed globally by different bodies to control the level of phosphorus concentrations into receiving environments. In order to satisfy the constraints, a high degree of tertiary treatment or at least a significant reduction of phosphorus concentration is obligatory. This comprehensive review summarizes phosphorus removal technologies, from the most commonly used conventional technologies such as chemical precipitation through metal addition, membrane filtration, reverse osmosis and enhanced biological phosphorus removal using activated sludge system to passive systems such as constructed wetlands and filtration systems. Trends, perspectives and scientific procedures conducted by different researchers have been presented. This review critically evaluates the advantages and limitations behind each of the technologies. Enhancement of passive systems using reactive media such as industrial wastes to provide additional uptake through adsorption or precipitation is also discussed in this article.

Keywords: adsorption, chemical precipitation, enhanced biological phosphorus removal, phosphorus removal

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Authors: Jeremy J. Johnson

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Mediterranean herbs including rosemary (Rosmarinus officinalis) contain a variety of phytochemicals including diterpenes that possess extensive biological activity. Applications of diterpenes, including the more abundant forms carnosol and carnosic acid, have been shown to possess anti-cancer, anti-inflammatory, anti-oxidant, and anti-proliferation properties. To confirm these properties, we have evaluated rosemary extract and selected diterpenes for biological activity in cancer and inflammatory models. Our preliminary data have revealed that select diterpenes can disrupt androgen receptor functionality in prostate and breast cancer cells. This property is unique among natural products for hormone-responsive cancers. The second area of interest has been evaluating rosemary extract and selected diterpenes for activation of sestrin-2, an antioxidant protein, in colon cancer cells. A combination of in vitro and in vivo approaches have been utilized to characterize the activity of rosemary diterpenes in rosemary. Taken together, these results suggest that phytochemicals found in rosemary have distinct pharmacological actions for disrupting cell-signaling pathways in cancer and inflammatory bowel disease.

Keywords: rosemary, diterpene, cancer, inflammation

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Authors: Md. Ruhul Amin

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The effects of CB1, CB3, CB5, CB8 and CB12 cotton varieties on the nutritional indices and biological parameters of armyworm Spodoptera litura were studied under laboratory conditions. The armyworm larvae showed the highest and lowest food consumption rates on CB8 and CB1 variety, respectively. The efficiency of the conversion of digested food, efficiency of conversion of ingested food, approximate digestibility rates were statistically higher and similar on CB5 and CB8, and lowest on CB1. The larvae reared on CB12 variety exerted the lowest feeding and growth indices, and the relative growth rate was highest on CB8. The survival rates of egg, larva, pupa and adult moths were found highest on CB8 and lowest on CB12. The development durations of the immature stages of the insect differed significantly and the time elapsed from egg-to-adult emergence, longevity of both male and female moths, and their lifecycle were shortest on CB12 variety. The nutritional indices and biological parameters of the armyworm indicated that the varieties CB5 and CB8 were suitable host plants for feeding and development of S. litura.

Keywords: gossypium hirsutum, spodoptera litura, food consumption, life history

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Authors: Manon Giraud, Francois-Damien Delapierre, Guenaelle Jasmin-Lebras, Cecile Feraudet-Tarisse, Stephanie Simon, Claude Fermon

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Early diagnosis or detection of harmful substances at low level is a growing field of high interest. The ideal test should be cheap, easy to use, quick, reliable, specific, and with very low detection limit. Combining the high specificity of antibodies-functionalized magnetic beads used to immune-capture biologic objects and the high sensitivity of a GMR-based sensors, it is possible to even detect these biologic objects one by one, such as a cancerous cell, a bacteria or a disease biomarker. The simplicity of the detection process makes its use possible even for untrained staff. Giant Magneto Resistance (GMR) is a recently discovered effect consisting in the electrical resistance modification of some conductive layers when exposed to a magnetic field. This effect allows the detection of very low variations of magnetic field (typically a few tens of nanoTesla). Magnetic nanobeads coated with antibodies targeting the analytes are mixed with a biological sample (blood, saliva) and incubated for 45 min. Then the mixture is injected in a very simple microfluidic chip and circulates above a GMR sensor that detects changes in the surrounding magnetic field. Magnetic particles do not create a field sufficient to be detected. Therefore, only the biological objects surrounded by several antibodies-functionalized magnetic beads (that have been captured by the complementary antigens) are detected when they move above the sensor. Proof of concept has been carried out on NS1 mouse cancerous cells diluted in PBS which have been bonded to magnetic 200nm particles. Signals were detected in cells-containing samples while none were recorded for negative controls. Binary response was hence assessed for this first biological model. The precise quantification of the analytes and its detection in highly diluted solution is the step now in progress.

Keywords: early diagnosis, giant magnetoresistance, lab-on-a-chip, submicron particle

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Authors: Ashwani Kumar Aggarwal

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NIR Light is non-ionizing and can pass easily through living tissues such as breast without any harmful effects. Therefore, use of NIR light for imaging the biological tissue and to quantify its optical properties is a good choice over other invasive methods. Optical tomography involves two steps. One is the forward problem and the other is the reconstruction problem. The forward problem consists of finding the measurements of transmitted light through the tissue from source to detector, given the spatial distribution of absorption and scattering properties. The second step is the reconstruction problem. In X-ray tomography, there is standard method for reconstruction called filtered back projection method or the algebraic reconstruction methods. But this method cannot be applied as such, in optical tomography due to highly scattering nature of biological tissue. A hybrid algorithm for reconstruction has been implemented in this work which takes into account the highly scattered path taken by photons while back projecting the forward data obtained during Monte Carlo simulation. The reconstructed image suffers from blurring due to point spread function. This blurred reconstructed image has been enhanced using a digital filter which is optimal in mean square sense.

Keywords: least-squares optimization, filtering, tomography, laser interaction, light scattering

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Authors: Hassiba Bougueria, Nesrine Benarous, Souheyla Chetioui

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Azo dyes are one of the most widely used compounds in organic chemistry, primarily due to their relatively simple preparation methods. They have therefore been widely used, in particular as colorants for textiles, printing inks, cosmetics, and food additives. In addition to their use as dyes, azo compounds have attracted much attention from chemists as their potential applications are important in coordination chemistry, metal-organic frameworks (MOF) structures, COF (covalent-organic frameworks), and catalysis. Moreover, they have found many applications in different fields, such as nonlinear optics, optical storage, photoluminescence, and magnetism. The compound bis{(E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalen-2-olato}copper(II) dimethyl sulfoxide monosolvate, the CuII atom is tetracoordinate with a square-planar geometry, surrounded by two bidentate (E)-1-[(2,4,6-tribromophenyl)diazenyl]naphthalene-2-olate ligands via two N atoms and two O atoms. The O-Cu-O angles and N-Cu-N are of the order of 177.90(16)° and 177.8(2)°, respectively. The distances Cu-O and Cu- N are 1.892(4) Å and 1.976(4) Å, respectively. The cohesion of the crystal is ensured by hydrogen bonds of the C—H…O type and by π=π staking interactions [centroid–centroid distance = 3.679(4)Å]. The DMSO solvent molecule is disordered at two positions with occupancy rates of 0.70 and 0.30.

Keywords: azo dyes, DRX, structural characterization, biological activity

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Authors: Deepa Gandhi, Pravin K. Naoghare, Amit Bafana, Krishnamurthi Kannan, Saravanadevi Sivanesana

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Oxidative stress is known to depreciate normal functioning of osteoblast cells. Present study reports oxidative/inflammatory signatures in fluoride exposed human osteosarcoma (HOS) cells and its possible association with the genes involved in bone developmental pathway. Microarray analysis was performed to understand the possible molecular mechanisms of stress-mediated bone lose in HOS cells. Cells were chronically exposed with sub-lethal concentration of fluoride. Global gene expression is profiling revealed 34 up regulated and 2598 down-regulated genes, which were associated with several biological processes including bone development, osteoblast differentiation, stress response, inflammatory response, apoptosis, regulation of cell proliferation. Microarray data were further validated through qRT-PCR and western blot analyses using key representative genes. Based on these findings, it can be proposed that chronic exposure of fluoride may impair bone development via oxidative and inflammatory stress. The present finding also provides important biological clues, which will be helpful for the development of therapeutic targets against diseases related bone.

Keywords: bone, HOS cells, microarray, stress

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Authors: Mehran Bakhshi, Mohammad Raouf Hosseini, Mohammadhosein Rahimi

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The cadmium sulfide nanoparticles were synthesized from the nickel-cadmium cake of a hydrometallurgical zinc producing plant and sodium sulfide as Cd²⁺ and S^-2 sources, respectively. Also, the synthesis process was performed by using the secretions of Bacillus licheniformis as bio-surfactant. Initially, in order to obtain a cadmium rich solution, two following steps were carried out: 1) Alkaline leaching for the removal of zinc oxide from the cake, and 2) acidic leaching to dissolve cadmium from the remained solid residue. Afterward, the obtained CdSO₄ solution was used for the nanoparticle biosynthesis. Nanoparticles were characterized by the energy dispersive spectroscopy (EDS) and X-ray diffraction (XRD) to confirm the formation of CdS crystals with cubic structure. Also, transmission electron microscopy (TEM) was applied to determine the particle sizes which were in 2-10 nm range. Moreover, the presence of the protein containing bio-surfactants was approved by using infrared analysis (FTIR). In addition, the absorbance below 400 nm confirms quantum particles’ size. Finally, it was shown that valuable CdS quantum dots could be obtained from the industrial waste products via environment-friendly biological approaches.

Keywords: biosynthesis, cadmium cake, cadmium sulfide, nanoparticle, zinc smelter

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Authors: Devarakonda Ramadevi, Dasari Rambabu, K. Suresh Babu, Battu Ganga Rao, Lakshmi Sirisha Kotikalapudi

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The phytochemical and biological evaluation of the whole plant of Derris scandens is belonging to the family fabaceae. The dried plant of D.scandens was procured from the tirumala. The completely dried powder of the whole plant was taken and ground to a coarse powder which was then subjected to Soxhlet extraction with hexane and chloroform successively for 36 hrs. Chloroform extract was filtered and concentrated by using rotary evaporator an about 100g extract was obtained. The chloroform extract was subjected to column chromatographed over silicagel. From the column chromatography seven compounds were isolated named as osajin, scandinone, scandenone, 4,5,7-tri hydroxy biprenyl isoflavone, derris isoflavone-A, scandenin and isoscandinone. D.scandens resulting in the isolation of seven compounds in the plant was confirmed by spectral data (1H NMR, 13C NMR, ESI-MS and FTIR). The isolated compounds were screened for antioxidant activity, antidiabetic activity, α-glucosidase (inhibitory activity) and anti-bacterial activity. The isolated seven compounds were tested for α-glucosidase inhibitory activity and antioxidant activity. All the seven compounds showed good α-glucosidase inhibitory activity and moderate antioxidant activity.

Keywords: Derris scandens, phytochemical, antioxident, antidiabetic, antibacterial activity

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