Search results for: microbial genomics

Authors: Dulanjali Ranasinghe, Isuru Supasan, Kaushalya Premachandra, Ranjan Dissanayake, Ajith Rajapaksha, Eustace Fernando

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Proteomics studies of organisms are considered to be significantly information-rich compared to their genomic counterparts because proteomes of organisms represent the expressed state of all proteins of an organism at a given time. In modern top-down and bottom-up proteomics workflows, the primary analysis methods employed are gel–based methods such as two-dimensional (2D) electrophoresis and mass spectrometry based methods. Machine learning (ML) and artificial intelligence (AI) have been used increasingly in modern biological data analyses. In particular, the fields of genomics, DNA sequencing, and bioinformatics have seen an incremental trend in the usage of ML and AI techniques in recent years. The use of aforesaid techniques in the field of proteomics studies is only beginning to be materialised now. Although there is a wealth of information available in the scientific literature pertaining to proteomics workflows, no comprehensive review addresses various aspects of the combined use of proteomics and machine learning. The objective of this review is to provide a comprehensive outlook on the application of machine learning into the known proteomics workflows in order to extract more meaningful information that could be useful in a plethora of applications such as medicine, agriculture, and biotechnology.

Keywords: proteomics, machine learning, gel-based proteomics, mass spectrometry

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Authors: Naijin Wu, Peizhong Li, Haijian Wang, Wenxia Wei, Yun Song

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Chlorinated aliphatic hydrocarbons (CAHs) pollution poses a severe threat to human health and is persistent in groundwater. Although chemical reduction or bioremediation is effective, it is still hard to achieve their complete and rapid dechlorination. Recently, the combination of zero-valent iron and biostimulation has been considered to be one of the most promising strategies, but field studies of this technology are scarce. In a typical site contaminated by various types of CAHs, basic physicochemical parameters of groundwater, CAHs and their product concentrations, and microbial abundance and diversity were monitored after a remediation slurry containing both micron zero-valent iron (mZVI) and biostimulation components were directly injected into the aquifer. Results showed that groundwater could form and keep low oxidation-reduction potential (ORP), a neutral pH, and anoxic conditions after different degrees of fluctuations, which was benefit for the reductive dechlorination of CAHs. The injection also caused an obvious increase in the total organic carbon (TOC) concentration and sulfate reduction. After 253 days post-injection, the mean concentration of total chlorinated ethylene (CEE) from two monitoring wells decreased from 304 μg/L to 8 μg/L, and total chlorinated ethane (CEA) decreased from 548 μg/L to 108 μg/L. Occurrence of chloroethane (CA) suggested that hydrogenolysis dechlorination was one of the main degradation pathways for CEA, and also hints that biological dechlorination was activated. A significant increase of ethylene at day 67 post-injection indicated that dechlorination was complete. Additionally, the total bacterial counts increased by 2-3 orders of magnitude after 253 days post-injection. And the microbial species richness decreased and gradually changed to anaerobic/fermentative bacteria. The relative abundance of potential degradation bacteria increased corresponding to the degradation of CAHs. This work demonstrates that mZVI and biostimulation can be combined to achieve the efficient removal of various CAHs from contaminated groundwater sources.

Keywords: chlorinated aliphatic hydrocarbons, groundwater, field study, zero-valent iron, biostimulation

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Authors: Manal Elgallal, Louise Fletcher, Barbara Evans

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Water scarcity is a growing concern in many arid and semi-arid countries. The increase of water scarcity threatens economic development and sustainability of human livelihoods as well as environment especially in developing countries. Globally, agriculture is the largest water consumption sector, accounting for approximately 70% of all freshwater extraction. Growing competition between the agricultural and higher economic value in urban and industrial uses of high-quality freshwater supplies, especially in regions where water scarcity major problems, will increase the pressure on this precious resource. In this circumstance, wastewater may provide reliable source of water for agriculture and enable freshwater to be exchanged for more economically valuable purposes. Concern regarding the risks from microbial and toxic components to human health and environment quality is a serious obstacle for wastewater reuse particularly in agriculture. Although powerful approaches and tools for microbial risk assessment and management for safe use of wastewater are now available, few studies have attempted to provide any mechanism to quantitatively assess and manage the environmental risks resulting from reusing wastewater. In seeking pragmatic solutions to sustainable wastewater reuse, there remains a lack of research incorporating both health and environmental risk assessment and management with economic analysis in order to quantitatively combine cost, benefits and risks to rank alternative reuse options. This study seeks to enhance effective reuse of wastewater for irrigation in arid and semi-arid areas, the outcome of the study is an evaluation approach that can be used to assess different reuse strategies and to determine the suitable scale at which treatment alternatives and interventions are possible, feasible and cost effective in order to optimise the trade-offs between risks to protect public health and the environment and preserving the substantial benefits.

Keywords: environmental risks, management, life cycle costs, waste water irrigation

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Authors: Muhammad Adeel Arshad, Shaukat Ali Bhatti, Faiz-ul Hassan

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Manipulating microbial ecosystem in the rumen is considered as an important strategy to optimize production efficiency in ruminants. In the past, antibiotics and synthetic chemical compounds have been used for the manipulation of rumen fermentation. However, since the non-therapeutic use of antibiotics has been banned, efforts are being focused to search out safe alternative products. In tropics, crop residues and forage grazing are major dietary sources for ruminants. Poor digestibility and utilization of these feedstuffs by animals is a limiting factor to exploit the full potential of ruminants in this area. Hence, there is a need to enhance the utilization of these available feeding resources. One of the potential strategies in this regard is the use of direct-fed microbes. Bacteria and fungi are mostly used as direct-fed microbes to improve animal health and productivity. Commonly used bacterial species include lactic acid-producing and utilizing bacteria (Lactobacillus, Streptococcus, Enterococcus, Bifidobacterium, and Bacillus) and fungal species of yeast are Saccharomyces and Aspergillus. Direct-fed microbes modulate microbial balance in the gastrointestinal tract through the competitive exclusion of pathogenic species and favoring beneficial microbes. Improvement in weight gain and feed efficiency has been observed as a result of feeding direct-fed bacteria. The use of fungi as a direct-fed microbe may prevent excessive production of lactate and harmful oxygen in the rumen leading to better feed digestibility. However, the mechanistic mode of action for bacterial or fungal direct-fed microbes has not been established yet. Various reports have confirmed an increase in dry matter intake, milk yield, and milk contents in response to the administration of direct-fed microbes. However, the application of a direct-fed microbe has shown variable responses mainly attributed to dosages and strains of microbes. Nonetheless, it is concluded that the inclusion of direct-fed microbes may mediate the rumen ecosystem to manage lactic acid production and utilization in both clinical and sub-acute rumen acidosis.

Keywords: microbes, roughages, rumen, feed efficiency, production, fermentation

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Authors: Jonathan Josephs-Spaulding, Hannah Rettig, Simon Graspeunter, Jan Rupp, Christoph Kaleta

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Background: Recurrent urinary tract infections (rUTIs) are a global cause of emergency room visits and represent a significant burden for public health systems. Therefore, metatranscriptomic approaches to investigate metabolic exchange and crosstalk between uropathogenic Escherichia coli (UPEC), which is responsible for 90% of UTIs, and collaborating pathogens of the urogenital microbiome is necessary to better understand the pathogenetic processes underlying rUTIs. Objectives: This study aims to determine the level in which uropathogens optimize the host urinary metabolic environment to succeed during invasion. By developing patient-specific metabolic models of infection, these observations can be taken advantage of for the precision treatment of human disease. Methods: To date, we have set up an rUTI patient cohort and observed various urine-associated pathogens. From this cohort, we developed patient-specific metabolic models to predict bladder microbiome metabolism during rUTIs. This was done by creating an in silico metabolomic urine environment, which is representative of human urine. Metabolic models of uptake and cross-feeding of rUTI pathogens were created from genomes in relation to the artificial urine environment. Finally, microbial interactions were constrained by metatranscriptomics to indicate patient-specific metabolic requirements of pathogenic communities. Results: Metabolite uptake and cross-feeding are essential for strain growth; therefore, we plan to design patient-specific treatments by adjusting urinary metabolites through nutritional regimens to counteract uropathogens by depleting essential growth metabolites. These methods will provide mechanistic insights into the metabolic components of rUTI pathogenesis to provide an evidence-based tool for infection treatment.

Keywords: recurrent urinary tract infections, human microbiome, uropathogenic Escherichia coli, UPEC, microbial ecology

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Authors: Tanushree Jaitly, Shailendra Gupta, Leila Taher, Gerold Schuler, Julio Vera

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Genomics-based personalized medicine is a promising approach to fight aggressive tumors based on patient's specific tumor mutation and expression profiles. A remarkable case is, dendritic cell-based immunotherapy, in which tumor epitopes targeting patient's specific mutations are used to design a vaccine that helps in stimulating cytotoxic T cell mediated anticancer immunity. Here we present a computational pipeline for epitope-based personalized cancer vaccines using patient-specific haplotype and cancer mutation profiles. In the workflow proposed, we analyze Whole Exome Sequencing and RNA Sequencing patient data to detect patient-specific mutations and their expression level. Epitopes including the tumor mutations are computationally predicted using patient's haplotype and filtered based on their expression level, binding affinity, and immunogenicity. We calculate binding energy for each filtered major histocompatibility complex (MHC)-peptide complex using docking studies, and use this feature to select good epitope candidates further.

Keywords: cancer immunotherapy, epitope prediction, NGS data, personalized medicine

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Authors: Andy Sand, Naama Massad – Ivanir, Nadav Nitzan, Elisa Valderrama, Alfred Wegenberger, Koranit Shlosman, Rotem Shemesh, Ester Segal

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Microbial spoilage of food products is of great concern in the food industry due to the direct impact on the shelf life of foods and the risk of foodborne illness. Therefore, food packaging may serve as a crucial contribution to keep the food fresh and suitable for consumption. Active packaging solutions that have the ability to inhibit the development of microorganism in food products attract a lot of interest, and many efforts have been made to engineer and assimilate such solutions on various food products. NanoPack is an EU-funded international project aiming to develop state-of-the-art antimicrobial packaging systems for perishable foods. The project is based on natural essential oils which possess significant antimicrobial activity against many bacteria, yeasts and molds. The essential oils are encapsulated in natural aluminosilicate clays, halloysite nanotubes (HNT's), that serves as a carrier for the volatile essential oils and enable their incorporation into polymer films. During the course of the project, several polyethylene films with diverse essential oils combinations were designed based on the characteristics of their target food products. The antimicrobial activity of the produced films was examined in vitro on a broad spectrum of microorganisms including gram-positive and gram-negative bacteria, aerobic and anaerobic bacteria, yeasts and molds. The films that showed promising in vitro results were successfully assimilated on in vivo active packaging of several food products such as cheese, bread, fruits and raw meat. The results of the in vivo analyses showed significant inhibition of the microbial spoilage, indicating the strong contribution of the NanoPack packaging solutions on the extension of shelf life and reduction of food waste caused by early spoilage throughout the supply chain.

Keywords: food safety, food packaging, essential oils, nanotechnology

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Authors: Simon Nyarko

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This study examined the microbial flora contamination of the Ghanaian paper currency notes and antibiotic resistance in Ejura Municipal, Ashanti Region, Ghana. This is a descriptive cross-sectional study designed to assess the profile of microflora contamination of the Ghanaian paper currency notes and antibiotic-resistant in the Ejura Municipality. The research was conducted in Ejura, a town in the Ejura Sekyeredumase Municipal of the Ashanti region of Ghana. 70 paper currency notes which were freshly collected from the bank, consisting of 15 pieces of GH ¢1, GH ¢2, and GH ¢5, 10 pieces of GH ¢10 and GH ¢20, and 5 pieces of GH ¢50, were randomly sampled from people by exchanging their money in usage with those freshly secured from the bank. The surfaces of each GH¢ note were gently swabbed and sent to the lab immediately in sterile Zip Bags and sealed, and tenfold serial dilution was inoculated on plate count agar (PCA), MacConkey agar (MCA), mannitol salt agar (MSA), and deoxycholate citrate agar (DCA). For bacterial identification, the study used appropriate laboratory and biochemical tests. The data was analyzed using SPSS-IBM version 20.0. It was found that 95.2 % of the 70 GH¢ notes tested positive for one or more bacterial isolates. On each GH¢ note, mean counts on PCA ranged from 3.0 cfu/ml ×105 to 4.8 cfu/ml ×105. Of 124 bacteria isolated. 36 (29.03 %), 32 (25.81%), 16 (12.90 %), 20 (16.13%), 13 (10.48 %), and 7 (5.66 %) were from GH¢1, GH¢2, GH¢10, GH¢5, GH¢20, and GH¢50, respectively. Bacterial isolates were Escherichia coli (25.81%), Staphylococcus aureus (18.55%), coagulase-negative Staphylococcus (15.32%), Klebsiella species (12.10%), Salmonella species (9.68%), Shigella species (8.06%), Pseudomonas aeruginosa (7.26%), and Proteus species (3.23%). Meat shops, commercial drivers, canteens, grocery stores, and vegetable shops contributed 25.81 %, 20.16 %, 19.35 %, 17.74 %, and 16.94 % of GH¢ notes, respectively. There was 100% resistance of the isolates to Erythromycin (ERY), and Cotrimoxazole (COT). Amikacin (AMK) was the most effective among the antibiotics as 75% of the isolates were susceptible to it. This study has demonstrated that the Ghanaian paper currency notes are heavily contaminated with potentially pathogenic bacteria that are highly resistant to the most widely used antibiotics and are a threat to public health.

Keywords: microflora, antibiotic resistance, staphylococcus aureus, culture media, multi-drug resistance

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Authors: Oustani Mabrouka, Halilat Med Tahar

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The physico-chemical properties of poultry droppings indicate that this waste can be an excellent way to enrich the soil with low fertility that is the case in arid soils (low organic matter content), but its concentrations in some microbial and chemical components make them potentially dangerous and toxic contaminants if they are used directly in fresh state. On other hand, the accumulation of plant residues in the crop areas can become a source of plant disease and affects the quality of the environment. The biotechnological processes that we have identified appear to alleviate these problems. It leads to the stabilization and processing of wastes into a product of good hygienic quality and high fertilizer value by the composting test. In this context, a trial was conducted in composting operations in the region of Ouargla located in southern Algeria. Composing test was conducted in a completely randomized design experiment. Three mixtures were prepared, in pits of 1 m3 volume for each mixture. Each pit is composed by mixture of poultry droppings and crushed plant residues in amount of 40 and 60% respectively: C1: Droppings + Straw (P.D +S) , C2: Poultry Droppings + Olive Wastes (P.D+O.W) , C3: Poultry Droppings + Date palm residues (P.D+D.P). Before and after the composting process, physico-chemical parameters (temperature, moisture, pH, electrical conductivity, total carbon and total nitrogen) were studied. The stability of the biological system was noticed after 90 days. The results of physico-chemical and microbiological compost obtained from three mixtures: C1: (P.D +S) , C2: (P.D+O.W) and C3: (P.D +D.P) shows at the end of composting process, three composts characterized by the final products were characterized by their high agronomic and environmental interest with a good physico chemical characteristics in particularly a low C/N ratio with 15.15, 10.01 and 15.36 % for (P.D + S), (P.D. + O.W) and (P.D. +D.P), respectively, reflecting a stabilization and maturity of the composts. On the other hand, a significant increase of temperature was recorded at the first days of composting for all treatments, which is correlated with a strong reduction of the pathogenic micro flora contained in poultry dropings.

Keywords: Arid environment, Composting, Date palm residues, Olive wastes, pH, Pathogenic microorganisms, Poultry Droppings, Straw

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Authors: Fuad Abdullah Alatawi

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Microbial infections-based diseases are a significant public health issue around the world, mainly when antibiotic-resistant bacterium types evolve. In this research, we explored the anti-bacterial and anti-cancer potency of iron-oxide (Fe₂O₃) nanoparticles prepared from F. macrocarpa fruit extract. The chemical composition of F. macrocarpa fruit extract was used as a reducing and capping agent for nanoparticles’ synthesis was examined by GC-MS/MS analysis. Then, the prepared nanoparticles were confirmed by various biophysical techniques, including X-ray powder diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), UV-Vis Spectroscopy, and Transmission Electron Microscopy (TEM) and Energy Dispersive Spectroscopy (EDAX), and Dynamic Light Scattering (DLS). Also, the antioxidant capacity of fruit extract was determined through 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), Fluorescence Recovery After Photobleaching (FRAP), Superoxide Dismutase (SOD) assays. Furthermore, the cytotoxicity activities of Fe₂O₃ NPs were determined using the (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) (MTT) test on MCF-7 cells. In the antibacterial assay, lethal doses of the Fe₂O₃NPs effectively inhibited the growth of gram-negative and gram-positive bacteria. The surface damage, ROS production, and protein leakage are the antibacterial mechanisms of Fe₂O₃NPs. Concerning antioxidant activity, the fruit extracts of F. macrocarpa had strong antioxidant properties, which were confirmed by DPPH, ABTS, FRAP, and SOD assays. In addition, the F. microcarpa-derived iron oxide nanomaterials greatly reduced the cell viability of (MCF-7). The GC-MS/MS analysis revealed the presence of 25 main bioactive compounds in the F. microcarpa extract. Overall, the finding of this research revealed that F. microcarpa-derived Fe₂O₃ nanoparticles could be employed as an alternative therapeutic agent to cure microbial infection and breast cancer in humans.

Keywords: ficus microcarpa, iron oxide, antibacterial activity, cytotoxicity

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Authors: Hai-Hong Gu, Yan-Jun Ai, Zheng Zhou

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Vanadium and titanium are rare metals with superior properties and are important resources in aerospace, aviation, and military. The vanadium/titanium magnetite are mostly ultra-lean ores, and a large number of tailings has been produced in the exploitation process. The tailings are characterized by loose structure, poor nutrient, complex composition and high trace metal contents. Returning green manure has been shown to not only increase plant biomass and soil nutrients but also change the bioavailability of trace metals and the microbial community structure. Fungi play an important role in decomposing organic matter and increasing soil fertility, and the application of organic matter also affects the community structure of fungi. The effects of green manure plants, alfalfa (Medicago sativa L.), returned to the tailings in situ on community structure of fungi, nutrients and bioavailability of trace metals in vanadium/titanium magnetite tailings were investigated in a pot experiment. The results showed that the fungal community diversity and richness were increase after alfalfa green manure returned in situ. The dominant phyla of the fungal community were Ascomycota, Basidiomycota and Ciliophora, especially, the phyla Ciliophora was rare in ordinary soil, but had been found to be the dominant phyla in tailings. Meanwhile, the nutrient properties and various trace metals may shape the microbial communities by affecting the abundance of fungi. It was found that the plant growth was stimulated and the available N and organic C were significantly improved in the vanadium/titanium magnetite tailing with the long-term returning of alfalfa green manure. Moreover, the DTPA-TEA extractable Cd and Zn concentrations in the vanadium/titanium magnetite tailing were reduced by 7.72%~23.8% and 8.02%~24.4%, respectively, compared with those in the non-returning treatment. The above results suggest that the returning of alfalfa green manure could be a potential approach to improve fungal community structure and restore mine tailing ecosystem.

Keywords: fungal community, green manure returning, vanadium/titanium magnet tailings, trace metals

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Authors: K. Premakumar, R. G. Lakmali, S. M. A. C. U. Senarathna

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In the present world, production and consumption of fruit and vegetable beverages have increased owing to the healthy life style of the people. Therefore, a study was conducted to develop composite vegetable squash by incorporating nutritional, medicinal and organoleptic properties of tomato, pumpkin and ginger. Considering the finding of several preliminary studies, five formulations in different combinations tomato pumpkin were taken and their physico-chemical parameters such as pH, TSS, titrable acidity, ascorbic acid content and total sugar and organoleptic parameters such as colour, aroma, taste, nature, overall acceptability were analyzed. Then the best sample was improved by using 1 % ginger (50% tomato+ 50% pumpkin+ 1% ginger). Best three formulations were selected for storage studied. The formulations were stored at 30 °C room temperature and 70-75% of RH for 12 weeks. Physicochemical parameters , organoleptic and microbial activity (total plate count, yeast and mold, E-coil) were analyzed during storage periods and protein content, fat content, ash were also analysed%.The study on the comparison of physico-chemical and sensory qualities of stored Squashes was done up to 12 weeks storage periods. The nutritional analysis of freshly prepared tomato pumpkin vegetable squash formulations showed increasing trend in titratable acidity, pH, total sugar, non -reducing sugar, total soluble solids and decreasing trend in ascorbic acid and reducing sugar with storage periods. The results of chemical analysis showed that, there were the significant different difference (p < 0.05) between tested formulations. Also, sensory analysis also showed that there were significant differences (p < 0.05) for organoleptic character characters between squash formulations. The highest overall acceptability was observed in formulation with 50% tomato+ 50% pumpkin+1% ginger and all the all the formulations were microbiologically safe for consumption. Based on the result of physico-chemical characteristics, sensory attributes and microbial test, the Composite Vegetable squash with 50% tomato+50% pumpkin+1% ginger was selected as best formulation and could be stored for 12 weeks without any significant changes in quality characteristics.

Keywords: nutritional analysis, formulations, sensory attributes, squash

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Authors: Apichaya Aneksampant, Xuefei Tu, Masami Fukushima, Mitsuo Yamamoto

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The restoration of seaweed beds recovery has been developed using a fertilization technique for supplying dissolved iron to barren coastal areas. The fertilizer is composed of iron oxides as a source of iron and compost as humic substance (HS) source, which can serve as chelator of iron to stabilize the dissolved species under oxic seawater condition. However, elution mechanisms of iron from iron oxide surfaces have not sufficiently elucidated. In particular, roles of microbial activities in the elution of iron from the fertilizer are not sufficiently understood. In the present study, a fertilizer (iron oxide/compost = 1/1, v/v) was incubated in a water tank at Mashike coast, Hokkaido Japan. Microorganisms in the 6-month fertilizer were isolated and identified as Exiguobacterium oxidotolerans sp. (T-2-2). The identified bacteria were inoculated to perform iron elution test in a postgate B medium, prepared in artificial seawater. Hematite was used as a model iron oxide and anthraquinone-2,7-disolfonate (AQDS) as a model for HSs. The elution test performed in presence and absence of bacteria inoculation. ICP-AES was used to analyze total iron and a colorimetric technique using ferrozine employed for the determination of ferrous ion. During the incubation period, sample contained hematite and T-2-2 in both presence and absence of AQDS continuously showed the iron elution and reached at the highest concentration after 9 days of incubation and then slightly decrease to stabilize within 20 days. Comparison to the sample without T-2-2, trace amount of iron was observed, suggesting that iron elution to seawater can be attributed to bacterial activities. The levels of total organic carbon (TOC) in the culture solution with hematite decreased. This may be to the adsorption of organic compound, AQDS, to hematite surfaces. The decrease in UV-vis absorption of AQDS in the culture solution also support the results of TOC that AQDS was adsorbed to hematite surfaces. AQDS can enhance the iron elution, while the adsorption of organic matter suppresses the iron elution from hematite.

Keywords: anthraquinone-2, 7-disolfonate, barren ground, E.oxidotolerans sp., hematite, humic substances, iron elution

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Authors: Malory Beaujolais

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Chlordecone is an organochlorine pesticide with a bishomocubane structure which led to high stability in organic matter. Microbial fuel cell is a type of electrochemical system that can convert organic matters into electricity thanks to electroactive bacteria. This technique has been used with mangrove swamp from Martinique to try to reduce chlordecone rates. Those experiments led to characterize the behavior of the electroactive biofilm formed at the cathode, without added redox mediator. The designed bioelectrochemical system seems to provide the necessary conditions for chlordecone degradation.

Keywords: bioelectrochemistry, bioremediation, chlordecone, mangrove swamp

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Authors: Peli̇n Yilmaz, Gi̇zemnur Yildiz Uysal, Emi̇ne Bi̇rci̇, Berk Özcan, Burak Koca, Ehsan Tuzcuoğlu, Fati̇h Kasap

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Development of Energy Efficient Programs (EEP) is one of the most significant trends in the wet appliance industry of the recent years. Thanks to the EEP, the energy consumption of a washing machine as one of the most energy-consuming home appliances can shrink considerably, while its washing performance and the textile hygiene should remain almost unchanged. Here in, the goal of the present study is to achieve an optimum EEP algorithm providing excellent textile hygiene results as well as cleaning performance in a domestic washing machine. In this regard, steam-pretreated cold wash approach with a combination of innovative algorithm solution in a relatively short washing cycle duration was implemented. For the parametric study, steam exposure time, washing load, total water consumption, main-washing time, and spinning rpm as the significant parameters affecting the textile hygiene and cleaning performance were investigated within a Design of Experiment study using Minitab 2021 statistical program. For the textile hygiene studies, specific loads containing the contaminated cotton carriers with Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa bacteria were washed. Then, the microbial removal performance of the designed programs was expressed as log reduction calculated as a difference of microbial count per ml of the liquids in which the cotton carriers before and after washing. For the cleaning performance studies, tests were carried out with various types of detergents and EMPA Standard Stain Strip. According to the results, the optimum EEP program provided an excellent hygiene performance of more than 2 log reduction of microorganism and a perfect Washing Efficiency Index (Iw) of 1.035, which is greater than the value specified by EU ecodesign regulation 2019/2023.

Keywords: washing machine, energy efficient programs, hygiene, washing efficiency index, microorganism, escherichia coli, staphylococcus aureus, pseudomonas aeruginosa, laundry

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Authors: Narin Salehiyan

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The later sequencing of the complete genomes of Mycoplasma genitalium and M. pneumoniae has pulled in significant consideration to the atomic science of mycoplasmas, the littlest self-replicating living beings. It shows up that we are presently much closer to the objective of defining, in atomic terms, the complete apparatus of a self-replicating cell. Comparative genomics based on comparison of the genomic cosmetics of mycoplasmal genomes with those of other microbes, has opened better approaches of looking at the developmental history of the mycoplasmas. There's presently strong hereditary bolster for the speculation that mycoplasmas have advanced as a department of gram-positive microbes by a handle of reductive advancement. Amid this prepare, the mycoplasmas misplaced significant parcels of their ancestors’ chromosomes but held the qualities basic for life. In this way, the mycoplasmal genomes carry a tall rate of preserved qualities, incredibly encouraging quality comment. The critical genome compaction that happened in mycoplasmas was made conceivable by receiving a parasitic mode of life. The supply of supplements from their has clearly empowered mycoplasmas to lose, amid advancement, the qualities for numerous assimilative forms. Amid their advancement and adjustment to a parasitic mode of life, the mycoplasmas have created different hereditary frameworks giving a profoundly plastic set of variable surface proteins to avoid the have safe framework.

Keywords: mycoplasma, plasma, pathogen, genome

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Authors: Tamanda Kamwendo

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The concept of benefit sharing has been a prominent global debate in the world, gaining traction in human research ethics. Despite its prevalence, the concept of benefit sharing is not without controversy over its meaning and justification. This is due to the fact that it lacks a broadly accepted definition and many proponents discuss benefit sharing by arguing for its necessity rather than engaging in critical intellectual engagement with technical issues such as what it implies. What is clear in the literature is that the underlying premise of benefit-sharing is that research involving underprivileged and marginalized people is currently unjust and inequitable because these people are denied access to these gains; thus, benefit-sharing arrangements are required for these research projects to be just and equitable. This paper, therefore, investigates the discourses and justifications behind the concept of benefit sharing to human participants, particularly when dealing with human genomics research. Furthermore, considering that benefit sharing is generally viewed as a transaction between research organizations and research participants, it raises ethical concerns concerning the commodification of human material and undermines the sanctity of the human genome. This is predicated on the idea that research sponsors would be compelled to deliver a minimum set of possible benefits to research participants and communities in exchange for their involvement in the study. There is, therefore, need to protect benefit-sharing practices in international health research by developing a governance legal framework. A legal framework of benefit sharing will also dispel the issue of commodification of human material where human genomic research is done.

Keywords: benefit sharing, human participants, human genomic research, ethical concerns

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Authors: Moatlhodi Wise Letshwenyo, Lesedi Lebogang

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Botswana is an arid country that needs to start reusing wastewater as part of its water security plan. Pilot scale slow sand filtration in combination with roughing filter was investigated for the treatment of effluent from Botswana International University of Science and Technology to meet Botswana irrigation standards. The system was operated at hydraulic loading rates of 0.04 m/hr and 0.12 m/hr. The results show that the system was able to reduce turbidity from 262 Nephelometric Turbidity Units to a range between 18 and 0 Nephelometric Turbidity Units which was below 30 Nephelometric Turbidity Units threshold limit. The overall efficacy ranged between 61% and 100%. Suspended solids, Biochemical Oxygen Demand, and Chemical Oxygen Demand removal efficiency averaged 42.6%, 45.5%, and 77% respectively and all within irrigation standards. Other physio-chemical parameters were within irrigation standards except for bicarbonate ion which averaged 297.7±44 mg L^-1 in the influent and 196.22±50 mg L^-1 in the effluent which was above the limit of 92 mg L^-1, therefore averaging a reduction of 34.1% by the system. Total coliforms, fecal coliforms, and Escherichia coli in the effluent were initially averaging 1.1 log counts, 0.5 log counts, and 1.3 log counts respectively compared to corresponding influent log counts of 3.4, 2.7 and 4.1, respectively. As time passed, it was observed that only roughing filter was able to reach reductions of 97.5%, 86% and 100% respectively for faecal coliforms, Escherichia coli, and total coliforms. These organism numbers were observed to have increased in slow sand filter effluent suggesting multiplication in the tank. Water quality index value of 22.79 for the physio-chemical parameters suggests that the effluent is of excellent quality and can be used for irrigation purposes. However, the water quality index value for the microbial parameters (1820) renders the quality unsuitable for irrigation. It is concluded that slow sand filtration in combination with roughing filter is a viable option for the treatment of secondary effluent for reuse purposes. However, further studies should be conducted especially for the removal of microbial parameters using the system.

Keywords: irrigation, slow sand filter, turbidity, wastewater reuse

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Authors: Ofonime U. M. John, Justina I. R. Udotong, Victor O. Nwaugo, Ime R. Udotong

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Oily wastes from oil and gas exploration and production (O&G E&P) activities were remediated for twelve weeks using Soil-Poultry dropping amendment. Culture-dependent microbiological, chemical and enzymatic techniques were employed to assess the efficacy of remediation process. Microbiological activities of the remediated wastes showed increased hydrocarbonoclastic microbial populations with increased remediation time; 2.7±0.1 x 105cfu/g to 8.3 ± 0.04 x106cfu/g for hydrocarbon utilizing bacteria, 1.7 ± 0.2 x103cfu/g to 6.0 ± 0.01 x 104cfu/g for hydrocarbon utilizing fungi and 2.2 ± 0.1 x 102cfu/g to 6.7 ± 0.1 x 103cfu/g for hydrocarbon utilizing actinomycetes. Bacteria associated with the remediated wastes after the remediation period included the genera Bacillus, Psuedomonas, Beijerinckia, Acinetobacter, Alcaligenes and Serratia. Fungal isolates included species of Penicillium, Aspergillus and Cladosporium, while the Actinomycetes included species of Rhodococcus, Nocardia and Streptomyces. Slight fluctuations in pH values between 6.5± 0.2 and 7.1 ± 0.08 were recorded throughout the process, while total petroleum hydrocarbon (TPH) content decreased from 89, 900 ± 0.03mg/kg to 425 ± 0.1 mg/kg after twelve weeks of remediation. The polycyclic aromatic hydrocarbon (PAH) levels decreased with increased remediation time; naphthalene, flourene, pheneanthrene, anthracene, pyrene, chrysene and benzo(b)flouranthene showed decreased values < 0.01 after twelve weeks of remediation. Enzyme activities revealed increased dehydrogenase and urease activities with increased remediation time and decreased phenol oxidase activity with increased remediation period. There was a positive linear correlation between densities of hydrocarbonoclastic microbes and dehydrogenase activity. On the contrary, phenol oxidase and urease activities showed negative correlation with microbial population. Results of this study confirmed that remediation of oily wastes using soil-poultry dropping amendment can result in eco-friendly O&G E&P wastes. It also indicates that urease and phenol oxidase activities can be reliable indices/tools to monitor PAH levels and rates of petroleum hydrocarbon degradation.

Keywords: dehydrogenase activity, oily wastes, remediation, soil-poultry dropping amendment

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Lamis Naddaf, Yuval Tabach

Abstract:

We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

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Authors: David Pinzauti, Simon De Jaegher, Maria D'Aguano, Manuele Biazzo

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The COVID-19 pandemic has left an indelible mark on global health, leading to a pressing need for understanding the intricate interactions between the virus and the human microbiome. This study focuses on characterizing the nasal microbiota of patients affected by COVID-19, with a specific emphasis on the comparison with unaffected individuals, to shed light on the crucial role of the microbiome in the development of this viral disease. To achieve this objective, Nanopore technology was employed to analyze the bacterial 16s rRNA full-length gene present in nasal swabs collected in Malta between January 2021 and August 2022. A comprehensive dataset consisting of 268 samples (126 SARS-negative samples and 142 SARS-positive samples) was subjected to a comparative analysis using an in-house, custom pipeline. The findings from this study revealed that individuals affected by COVID-19 possess a nasal microbiota that is significantly less diverse, as evidenced by lower α diversity, and is characterized by distinct microbial communities compared to unaffected individuals. The beta diversity analyses were carried out at different taxonomic resolutions. At the phylum level, Bacteroidota was found to be more prevalent in SARS-negative samples, suggesting a potential decrease during the course of viral infection. At the species level, the identification of several specific biomarkers further underscores the critical role of the nasal microbiota in COVID-19 pathogenesis. Notably, species such as Finegoldia magna, Moraxella catarrhalis, and others exhibited relative abundance in SARS-positive samples, potentially serving as significant indicators of the disease. This study presents valuable insights into the relationship between COVID-19 and the nasal microbiota. The identification of distinct microbial communities and potential biomarkers associated with the disease offers promising avenues for further research and therapeutic interventions aimed at enhancing public health outcomes in the context of COVID-19.

Keywords: COVID-19, nasal microbiota, nanopore technology, 16s rRNA gene, biomarkers

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Authors: Ariel Vilchez, Francisca Acevedo, Rodrigo Navia

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The wound healing process can be accelerated and improved by the action of antioxidants such as curcumin (Cur) over the tissues; however, the efficacy of curcumin used through the digestive system is not enough to exploit its benefits. Electrospinning presents an alternative to carry curcumin directly to the wounds, and polyhydroxybutyrate (PHB) is proposed as the matrix to load curcumin owing to its biodegradable and biocompatible properties. PHB is among 150 types of Polyhydroxyalkanoates (PHAs) identified, it is a natural thermoplastic polyester produced by microbial fermentation obtained from microorganisms. The proposed objective is to develop electrospun bacterial PHB-based microfibers containing curcumin for possible biomedical applications. Commercial PHB was solved in Chloroform: Dimethylformamide (4:1) to a final concentration of 7% m/V. Curcumin was added to the polymeric solution at 1%, and 7% m/m regarding PHB. The electrospinning equipment (NEU-BM, China) with a rotary collector was used to obtain Cur-PHB fibers at different voltages and flow rate of the polymeric solution considering a distance of 20 cm from the needle to the collector. Scanning electron microscopy (SEM) was used to determine the diameter and morphology of the obtained fibers. Thermal stability was obtained from Thermogravimetric (TGA) analysis, and Fourier Transform Infrared Spectroscopy (FT-IR) was carried out in order to study the chemical bonds and interactions. A preliminary curcumin release to Phosphate Buffer Saline (PBS) pH = 7.4 was obtained in vitro and measured by spectrophotometry. PHB fibers presented an intact chemical composition regarding the original condition (dust) according to FTIR spectra, the diameter fluctuates between 0.761 ± 0.123 and 2.157 ± 0.882 μm, with different qualities according to their morphology. The best fibers in terms of quality and diameter resulted in sample 2 and sample 6, obtained at 0-10kV and 0.5 mL/hr, and 0-10kV and 1.5 mL/hr, respectively. The melting temperature resulted near 178 °C, according to the bibliography. The crystallinity of fibers decreases while curcumin concentration increases for the studied interval. The curcumin release reaches near 14% at 37 °C at 54h in PBS adjusted to a quasi-Fickian Diffusion. We conclude that it is possible to load curcumin in PHB to obtain continuous, homogeneous, and solvent-free microfibers by electrospinning. Between 0% and 7% of curcumin, the crystallinity of fibers decreases as the concentration of curcumin increases. Thus, curcumin enhances the flexibility of the obtained material. HPLC should be used in further analysis of curcumin release.

Keywords: antioxidant, curcumin, polyhydroxybutyrate, wound healing

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Authors: Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani

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Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. This method presented here works to augment existing regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. This method is applied on a time-series RNA-Seq data set from Escherichia coli as it transitions from growth to stationary phase over five hours. Investigations are conducted on the various metabolic activities in gene regulation processes by taking advantage of the correlation between regulatory gene pairs to examine their activity on a dynamic network. Especially, the changes in metabolic activity during phase transition are analyzed with focus on the pagP gene as well as other associated transcription factors. The visualization of the sequential transcriptional activity is used to describe the change in metabolic pathway activity originating from the pagP transcription factor, phoP. The results show a shift from amino acid and nucleic acid metabolism, to energy metabolism during the transition to stationary phase in E. coli.

Keywords: Escherichia coli, gene regulation, network, time-series

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Authors: Nieto Bernal Wilson, Carmona Suarez Edgar

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The organizations have structured and unstructured information in different formats, sources, and systems. Part of these come from ERP under OLTP processing that support the information system, however these organizations in OLAP processing level, presented some deficiencies, part of this problematic lies in that does not exist interesting into extract knowledge from their data sources, as also the absence of operational capabilities to tackle with these kind of projects.  Data Warehouse and its applications are considered as non-proprietary tools, which are of great interest to business intelligence, since they are repositories basis for creating models or patterns (behavior of customers, suppliers, products, social networks and genomics) and facilitate corporate decision making and research. The following paper present a structured methodology, simple, inspired from the agile development models as Scrum, XP and AUP. Also the models object relational, spatial data models, and the base line of data modeling under UML and Big data, from this way sought to deliver an agile methodology for the developing of data warehouses, simple and of easy application. The methodology naturally take into account the application of process for the respectively information analysis, visualization and data mining, particularly for patterns generation and derived models from the objects facts structured.

Keywords: data warehouse, model data, big data, object fact, object relational fact, process developed data warehouse

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Authors: Nandhana Vivek, Bhaskar Gogoi, Ayyavu Mahesh

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Breast cancer metastasis plays a key role in cancer progression and fatality. The present study examines the potential causes of metastasis in breast cancer by investigating the novel interactions between genes and their pathways. The gene expression profile of GSE99394, GSE1246464, and GSE103865 was downloaded from the GEO data repository to analyze the differentially expressed genes (DEGs). Protein-protein interactions, target factor interactions, pathways and gene relationships, and functional enrichment networks were investigated. The proliferation pathway was shown to be highly expressed in breast cancer progression and metastasis in all three datasets. Gene Ontology analysis revealed 11 DEGs as gene targets to control breast cancer metastasis: LYN, DLGAP5, CXCR4, CDC6, NANOG, IFI30, TXP2, AGTR1, MKI67, and FTH1. Upon studying the function, genomic and proteomic data, and pathway involvement of the target genes, DLGAP5 proved to be a promising candidate due to it being highly differentially expressed in all datasets. The study takes a unique perspective on the avenues through which DLGAP5 promotes metastasis. The current investigation helps pave the way in understanding the role DLGAP5 plays in metastasis, which leads to an increased incidence of death among breast cancer patients.

Keywords: genomics, metastasis, microarray, cancer

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: Ahmad Ali, Muhammad Imran Ghani, Haiyan Ding, Zhihui Cheng, Muhammad Iqbal

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Background and Aims: In recent years, protected cultivation trend, especially in the northern parts of China, spread dynamically where production area, structure, and crops diversity have expanded gradually under plastic greenhouse vegetable cropping (PGVC) system. Under this growing system, continuous monoculture with excessive synthetic fertilizers inputs are common cultivation practices frequently adopted by commercial producers. Such long-term cumulative wild exercise year after year sponsor the continuous cropping obstacles in PGVC soil, which have greatly threatened the regional soil eco-sustainability and further impose the continuous assault on soil ecological diversity leading to the exhaustion of agriculture productivity. The aim of this study was to develop new allelopathic insights by exploiting available biological resources in the favor of sustainable PGVC to illuminate the continuous obstacle factors in plastic greenhouse. Method: A greenhouse study was executed under plastic tunnel located at the Horticulture Experimental Station of the College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, one of the prominent regions for intensive commercial PGVC in China. Post-harvest garlic residues (stalk, leaves) mechanically smashed, homogenized into powder size and incorporated at the ratio of 1:100; 3:100; 5:100 as a soil amendment in a replanted soil that have been used for continuous cucumber monoculture for 7 years (annually double cropping system in a greenhouse). Results: Incorporated C-rich garlic stalk significantly influenced the soil condition through various ways; organic matter decomposition and mineralization, moderately adjusted the soil pH, enhanced the soil nutrient availability, increased enzymatic activities, and promoted 20% more cucumber yield in short-time. Using Illumina MiSeq sequencing analysis of bacterial 16S rRNA and fungal 18S rDNA genes, the current study revealed that addition of garlic stalk/residue could also improve the microbial abundance and community composition in extensively exploited soil, and contributed in soil functionality, caused prosper changes in soil characteristics, reinforced to good crop yield. Conclusion: Our study provided evidence that addition of garlic stalk as soil fertility amendment is a feasible, cost-effective and efficient resource utilization way for renovation of degraded soil health, ameliorate soil quality components and improve ecological environment in short duration. Our study may provide a better scientific understanding for efficient crop residue management typically from allelopathic source.

Keywords: garlic stalk, microbial community dynamics, plant growth, soil amendment, soil-plant system

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Authors: Fatemeh Nokhodchi Bonab

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Bioinformatics, in its broad sense, involves application of computer processes to solve biological problems. A wide range of computational tools are needed to effectively and efficiently process large amounts of data being generated as a result of recent technological innovations in biology and medicine. A number of computational tools have been developed or adapted to deal with the experimental riches of complex and multivariate data and transition from data collection to information or knowledge. These bioinformatics tools are being evaluated and applied in various medical areas including early detection, risk assessment, classification, and prognosis of cancer. The goal of these efforts is to develop and identify bioinformatics methods with optimal sensitivity, specificity, and predictive capabilities. The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems.

Keywords: methods, applications, transcriptional regulatory systems, techniques

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Authors: R. H. Bustos, L. Martinez, J. García, F. Suárez

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MRP1 (Multi-drug resistance associated protein 1) and MRP2 (Multi-drug resistance associated protein 2) are two proteins belonging to the transporters of ABC (ATP-Binding Cassette). These transporter proteins are involved in the efflux of several biological drugs and xenobiotic and also in multiple physiological, pathological and pharmacological processes. Evidence has been found that there is a correlation among different polymorphisms found and their clinical implication in the resistance to antiepileptic, chemotherapy and anti-infectious drugs. In our study, exonic regions of MRP1/ABCC1 y MRP2/ABCC2 were studied in the Colombian population, specifically in the region of the central Savannah (Cundinamarca) to determinate SNP (Single Nucleotide Polymorphisms) and determinate its allele frequency and its genomics frequency. Results showed that for our population, SNP are found that have been previously reported for MRP1/ABCC1 (rs200647436, rs200624910, rs150214567) as well as for MRP2/ABCC2 (rs2273697, rs3740066, rs142573385, rs17216212). In addition, 13 new SNP were identified. Evidences show an important clinic correlation for polymorphisms rs3740066 and rs2273697. The study object population displays genetic variability as compared to the one reported in other populations.

Keywords: ATP-binding cassette (ABCC), Colombian population, multidrug-resistance protein (MRP), pharmacogenetic, single nucleotide polymorphism (SNP)

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