Search results for: molecular microbial methods

Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: biosensor, DNA, biomarker, molecular dynamics simulation

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Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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Authors: Mariam Azam, Sajjad Ur Rahman, Mukarram Bashir, Muhammad Tahir, Seemal Javaid, Jawad, Aoun Muhammad, Muhammad Zohaib, Hannan Khan

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Products of microbial origin are of great importance as they have proved their value in healthcare and nutrition, use of these microbial metabolites acquired from partially fermented soya hulls and wheat bran along with Saccharomyces cerevisiae (DL-22 S/N) substantiates to be a great source for an increase in the total milk production and quality yield.1×109 CFU/ml cells of Saccharomyces cerevisiae (DL-22 S/N) were further grown under in-vivo conditions for the assessment of quality milk production. Two groups with twelve cows, each having the same physical characteristics (Group A and Group B), were under study, Group A was daily fed with 12gm of biological metabolites and 22% protein-pelleted feed. On the other hand, the animals of Group B were provided with no metabolites in their feed. In thirty days of trial, improvement in the overall health, body score, milk protein, milk fat, yield, incidence rate of mastitis, ash, and solid not fat (SNF) was observed. The collected data showed that the average quality milk production was elevated up to 0.45 liter/h/d. However, a reduction in the milk fats up to 0.45% and uplift in the SNF value up to 0.53% of cow milk was also observed. At the same time, the incidence rate of mastitis recorded for the animals under trial was reduced to half, and improved non specific immunity was reported.

Keywords: microbial metabolites, post-biotics, animal supplements, animal nutrition, proteins, animal production, fermentation

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Authors: Chabungbam Niranjit Khuman, Makarand Madhao Ghangrekar, Arunabha Mitra

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The cost of aeration is one of the limiting factors in the upscaling of microbial fuel cells (MFC) for field-scale applications. Wetland macrophytes have the ability to release oxygen into the water to maintain aerobic conditions in their root zone. In this experiment, the efficacy of rhizospheric oxygen release of wetland macrophytes as a source of oxygen in the cathodic chamber of MFC was conducted. The experiment was conducted in an MFC consisting of a three-liter anodic chamber made of ceramic cylinder and a 27 L cathodic chamber. Untreated carbon felts were used as electrodes (i.e., anode and cathode) and connected to an external load of 100 Ω using stainless steel wire. Wetland macrophytes (Canna indica) were grown in the cathodic chamber of the MFC in a hydroponic fashion using a styrofoam sheet (termed as macrophytes assisted-microbial fuel cell, M-MFC). The catholyte (i.e., water) in the M-MFC had negligible contact with atmospheric air due to the styrofoam sheet used for maintaining the hydroponic condition. There was no mixing of the catholyte in the M-MFC. Sucrose based synthetic wastewater having chemical oxygen demand (COD) of 3000 mg/L was fed into the anodic chamber of the MFC in fed-batch mode with a liquid retention time of four days. The C. indica thrived well throughout the duration of the experiment without much care. The average dissolved oxygen (DO) concentration and pH value in the M-MFC were 3.25 mg/L and 7.07, respectively, in the catholyte. Since the catholyte was not in contact with air, the DO in the catholyte might be considered as solely liberated from the rhizospheric oxygen release of C. indica. The maximum COD removal efficiency of M-MFC observed during the experiment was 76.9%. The inadequacy of terminal electron acceptor in the cathodic chamber in M-MFC might have hampered the electron transfer, which in turn, led to slower specific microbial activity, thereby resulting in lower COD removal efficiency than the traditional MFC with aerated catholyte. The average operating voltage (OV) and open-circuit voltage (OCV) of 294 mV and 594 mV, respectively, were observed in M-MFC. The maximum power density observed during polarization was 381 mW/m³, and the maximum sustainable power density observed during the experiment was 397 mW/m³ in M-MFC. The maximum normalized energy recovery and coulombic efficiency of 38.09 Wh/m³ and 1.27%, respectively, were observed. Therefore, it was evidenced that rhizospheric oxygen release of wetland macrophytes (C. indica) was capable of sustaining the cathodic reaction in MFC for field-scale applications.

Keywords: hydroponic, microbial fuel cell, rhizospheric oxygen release, wetland macrophytes

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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: Mahmoud A. Abdulhamid

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Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

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Authors: Andrea Pietrelli, Vincenzo Ferrara, Bruno Allard, Francois Buret, Irene Bavasso, Nicola Lovecchio, Francesca Costantini, Firas Khaled

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This paper aims to show some applications of microbial fuel cells (MFCs), an energy harvesting technique, as clean power source to supply low power device for application like wireless sensor network (WSN) for environmental monitoring. Furthermore, MFC can be used directly as biosensor to analyse parameters like pH and temperature or arranged in form of cluster devices in order to use as small power plant. An MFC is a bioreactor that converts energy stored in chemical bonds of organic matter into electrical energy, through a series of reactions catalysed by microorganisms. We have developed a lab-scale terrestrial microbial fuel cell (TMFC), based on soil that acts as source of bacteria and flow of nutrient and a lab-scale waste water microbial fuel cell (WWMFC), where waste water acts as flow of nutrient and bacteria. We performed large series of tests to exploit the capability as biosensor. The pH value has strong influence on the open circuit voltage (OCV) delivered from TMFCs. We analyzed three condition: test A and B were filled with same soil but changing pH from 6 to 6.63, test C was prepared using a different soil with a pH value of 6.3. Experimental results clearly show how with higher pH value a higher OCV was produced; indeed reactors are influenced by different values of pH which increases the voltage in case of a higher pH value until the best pH value of 7 is achieved. The influence of pH on OCV of lab-scales WWMFC was analyzed at pH value of 6.5, 7, 7.2, 7.5 and 8. WWMFCs are influenced from temperature more than TMFCs. We tested the power performance of WWMFCs considering four imposed values of ambient temperature. Results show how power performance increase proportionally with higher temperature values, doubling the output power from 20° to 40°. The best value of power produced from our lab-scale TMFC was equal to 310 μW using peaty soil, at 1KΩ, corresponding to a current of 0.5 mA. A TMFC can supply proper energy to low power devices of a WSN by means of the design of three stages scheme of an energy management system, which adapts voltage level of TMFC to those required by a WSN node, as 3.3V. Using a commercial DC/DC boost converter, that needs an input voltage of 700 mV, the current source of 0.5 mA, charges a capacitor of 6.8 mF until it will have accumulated an amount of charge equal to 700 mV in a time of 10 s. The output stage includes an output switch that close the circuit after a time of 10s + 1.5ms because the converter can boost the voltage from 0.7V to 3.3V in 1.5 ms. Furthermore, we tested in form of clusters connected in series up to 20 WWMFCs, we have obtained a high voltage value as output, around 10V, but low current value. MFC can be considered a suitable clean energy source to be used to supply low power devices as a WSN node or to be used directly as biosensor.

Keywords: energy harvesting, low power electronics, microbial fuel cell, terrestrial microbial fuel cell, waste-water microbial fuel cell, wireless sensor network

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Oluwatofunmi Musa-Ajakaiye, Paul Olorunfemi M.D MPH, John Obafaiye

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Introduction: The U.S Food and Drug Administration (FDA) reports the public notices for recalled FDA-regulated products over periods of time. It study reviewed the primary reasons for recalls of products of various types over a period of 7 years. Methods: The study analyzed data provided in the FDA’s archived recalls for the years 2010-2017. It identified the various reasons for product recalls in the categories of foods, beverages, drugs, medical devices, animal and veterinary products, and dietary supplements. Using SPSS version 29, descriptive statistics and chi-square analysis of the data were performed. Results (numbers, percentages, p-values, chi-square): Over the period of analysis, a total of 931 recalls were reported. The most frequent reason for recalls was undeclared products (36.7%). The analysis showed that the most recalled product type in the data set was foods and beverages, representing 591 of all recalled products (63.5%).In addition, it was observed that foods and beverages represent 77.2% of products recalled due to the presence of microorganisms. Also, a sub-group analysis of recall reasons of food and beverages found that the most prevalent reason for such recalls was undeclared products (50.1%) followed by Listeria (17.3%) then Salmonella (13.2%). Conclusion: This analysis shows that foods and beverages have the greatest percentages of total recalls due to the presence of undeclared products listeria contamination and Salmonella contamination. The prevalence of Salmonella and Listeria contamination suggests that there is a high risk of microbial contamination in FDA-approved products and further studies on the effects of such contamination must be conducted to ensure consumer safety.

Keywords: food, beverages, listeria, salmonella, FDA, contamination, microbial

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Bengi Hakguder Taze, Sevcan Unluturk

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Şalak apricot (Prunus armeniaca L., cv. Şalak) is a specific variety grown in Igdir, Turkey. The fruit has distinctive properties distinguish it from other cultivars, such as its unique size, color, taste and higher water content. Drying is the widely used method for preservation of apricots. However, fresh consumption is preferred for Şalak apricot instead of drying due to its low dry matter content. Higher amounts of water in the structure and climacteric nature make the fruit sensitive against rapid quality loss during storage. Hence, alternative processing methods need to be introduced to extend the shelf life of the fresh produce. Mild heat (MH) treatment is of great interest as it can reduce the microbial load and inhibit enzymatic activities. Therefore, the aim of this study was to evaluate the impact of mild heat treatment on the natural microflora found on Şalak apricot surfaces and some physical quality parameters of the fruit, such as color and firmness. For this purpose, apricot samples were treated at different temperatures between 40 and 60 ℃ for different periods ranging between 10 to 60 min using a temperature controlled water bath. Natural flora on the fruit surfaces was examined using standard plating technique both before and after the treatment. Moreover, any changes in color and firmness of the fruit samples were also monitored. It was found that control samples were initially containing 7.5 ± 0.32 log CFU/g of total aerobic plate count (TAPC), 5.8±0.31 log CFU/g of yeast and mold count (YMC), and 5.17 ± 0.22 log CFU/g of coliforms. The highest log reductions in TAPC and YMC were observed as 3.87-log and 5.8-log after the treatments at 60 ℃ and 50 ℃, respectively. Nevertheless, the fruit lost its characteristic aroma at temperatures above 50 ℃. Furthermore, great color changes (ΔE ˃ 6) were observed and firmness of the apricot samples was reduced at these conditions. On the other hand, MH treatment at 41 ℃ for 10 min resulted in 1.6-log and 0.91-log reductions in TAPC and YMC, respectively, with slightly noticeable changes in color (ΔE ˂ 3). In conclusion, application of temperatures higher than 50 ℃ caused undesirable changes in physical quality of Şalak apricots. Although higher microbial reductions were achieved at those temperatures, temperatures between 40 and 50°C should be further investigated considering the fruit quality parameters. Another strategy may be the use of high temperatures for short time periods not exceeding 1-5 min. Besides all, MH treatment with UV-C light irradiation can be also considered as a hurdle strategy for better inactivation results.

Keywords: color, firmness, mild heat, natural flora, physical quality, şalak apricot

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Authors: Serap Gedikli, Hakan Çakmak, M. Buğra Güldiken, Duygu Yalnızoğlu

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Air, which is necessary for living things to survive; while it carries some useful substances in it, it can also carry foreign particles of different sizes that may be harmful to the health. All airborne organic substances of biological origin, including bacteria, fungi, fungal spores, viruses, pollen, and their components, are called "bioaerosols". Nowadays, everyone spends most of their time in closed areas such as home, workplace, school, etc. Although it is known that outdoor air pollution affects health, it is not known that indoor air pollution has harmful effects in terms of health. In this study, indoor air microbial load and SARS-CoV-2 virus cleaning efficiency of Froumann brand air cleaners were studied. This work in 300 m³, 600 m³, and 1000 m³ completely closed areas without any air circulation with Froumann N80, N90, and N100 air-cleaning devices. Analyzes were performed for both areas at 60 minutes before and after the device was operated using a particle measuring device (Particles Plus 7302) and an air sampler (Mas-100 ECO). The measurements were taken by placing the test equipment 1.5-2 m away from the air cleaner. At the same time, the efficiency of the HEPA filter was evaluated by taking samples from the air outlet point of the HEPA filter using the air sampling device (Mas-100 ECO) after the device was started. Nutrient agar and malt agar are used as total mesophilic bacteria and total fungi. The number of colony-forming units per m³ (cfu/m³) was calculated by counting colonies in Petri dishes after incubation for 48 hours at 37°C for bacteria and 72 hours at 30°C for fungi. The change in the number of colonies and the decrease in the microbial load was calculated as a percentage value. SARS-CoV-2 activity analysis studies were carried out by İnönü University Microbiology Department in accordance with the World Health Organization regulations. Finally, the HEPA filter in the devices used was taken and kept under a certain temperature and humidity, and the change in the microbial load on it was monitored over a 6-month period. At the end of the studies, a 91%-94% reduction was determined in the total mesophilic bacteria count of Frouman brand N80, N90, and N100 model air cleaners. A decrease of 94%-96% was detected in the total number of yeast/molds. HEPA filter efficiency was evaluated, and at the end of the analysis, 98% of the bacterial load and approximately 100% of yeast/mold load at the HEPA filter air outlet point were decreased. According to the SARS- CoV-2 analysis results, when the device is operating at the medium airflow level 3, it can filter virus-carrying aerosols by 99%. As a result, it was determined that the Froumann model air cleaner was effective in controlling and reducing the microbial load in the indoor air.

Keywords: HEPA filter, indoor air quality, microbial load, SARS-CoV-2

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Authors: Prachi Choudhary, Jai Gopal Sharma

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Microbial cultures determine the type of organism, its abundance in the tested sample, or both. It is one of the primary diagnostic methods of microbiology. It is used to determine the cause of infectious disease by letting the agent multiply in a predetermined medium. Different bacteria produce colonies that may be very distinct from the bacterial species that produced them. To culture any pathogen or microorganism, we should first know about the types of media used in microbiology for culturing. Sometimes sub culturing is also done in various microorganisms if some mixed growth is seen in culture. Nearly 3 types of culture media based on consistency – solid, semi-solid, and liquid (broth) media; are further explained in the report. Then, The Five I's approach is a method for locating, growing, observing, and characterizing microorganisms, including inoculation and incubation. Isolation, inspection, and identification. For identification of bacteria, we have to culture the sample like urine, sputum, blood, etc., on suitable media; there are different methods of culturing the bacteria or microbe like pour plate method, streak plate method, swabbing by needle, pipetting, inoculation by loop, spreading by spreader, etc. After this, we see the bacterial growth after incubation of 24 hours, then according to the growth of bacteria antibiotics susceptibility test is conducted; this is done for sensitive antibiotics or resistance to that bacteria, and also for knowing the name of bacteria. Various methods like the dilution method, disk diffusion method, E test, etc., do antibiotics susceptibility tests. After that, various medicines are provided to the patients according to antibiotic sensitivity and resistance.

Keywords: inoculation, incubation, isolation, antibiotics suspectibility test, characterizing

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Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Sangram Dhumal, Anil Karale

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The effect of different pretreatments and modified atmosphere packaging on the quality of minimally processed pomegranate arils of Bhagwa cultivar was evaluated during storage at 1⁰C for 16 days. Hand extracted pomegranate arils were pretreated with different antioxidants and surfactants viz., 100ppm sodium hypochlorite plus 0.5 percent ascorbic acid plus 0.5 percent citric acid, 10 and 20 percent honey solution, 0.1 percent nanosilver stipulated food grade hydrogen peroxide alone and in combination with 10 percent honey solution and control. The disinfected, rinsed and air-dried pomegranate arils were packed in polypropylene punnets (135g each) with different modified atmospheres and stored up to 16 days at 1⁰C. Changes in colour, pH, total soluble solids, sugars, anthocyanins, phenols, acidity, antioxidant activity, microbial and yeast and mold count over initial values were recorded in all the treatments under study but highest on those without antioxidant and surfactant treatments. Pretreated arils stored at 1⁰C recorded decrease in L*, b* value, pH, levels of non-reducing and total sugars, polyphenols, antioxidant activity and acceptability of arils and increase in total soluble solids, a* value, anthocyanins and microbial count. Increase in anthocyanin content was observed in modified atmosphere packaged pretreated arils stored at 1⁰C. Modified atmosphere packaging with 100 percent nitrogen recorded minimum changes in physicochemical and sensorial parameters with minimum microbial growth. Untreated arils in perforated punnets and with air (control) gave shelf life up to 6 days only. The pretreatment of arils with 10 percent honey plus 0.1 percent nanosilver stipulated food grade hydrogen peroxide and packaging in 100 percent nitrogen recorded minimum changes in physicochemical parameters. The treatment also restricted microbial growth and maintained colour, anthocyanin pigmentation, antioxidant activity and overall fresh like quality of arils. The same dipping treatment along with modified atmosphere packaging extended the shelf life of fresh ready to eat arils up to 14 to 16 days with enhanced acceptability when stored at 1⁰C.

Keywords: anthocyanin content, pomegranate, MAP, minimally processed, microbial quality, Bhagwa, shelf-life, overall quality

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Authors: Micheale Yifter Weldemichael

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

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Authors: Ayuko Itsuki, Sachiyo Aburatani

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Soil neutral sugar contents in Kasuga-yama Hill Primeval Forest (Nara, Japan) were examined using the Waksman’s approximation analysis to clarify relations with the neutral sugar constituted the soil organic matter and the microbial biomass. Samples were selected from the soil surrounding laurel-leaved (BB-1) and Carpinus japonica (BB-2) trees for analysis. The water and HCl soluble neutral sugars increased microbial biomass of the laurel-leaved forest soil. Arabinose, xylose, and galactose of the HCl soluble fraction were used immediately in comparison with other neutral sugars. Rhamnose, glucose, and fructose of the HCl soluble fraction were re-composed by the microbes.

Keywords: forest soil, neutral sugaras, soil organic matter, Waksman’s approximation analysis

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Authors: Deeba N. Baig, Ateeqa Ijaz, Saloome Rafiq

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Camel is a religious and culturally significant animal in Asian and African regions. In Pakistan Dromedary and Bactrian are common camel breeds. Other than the transportation use, it is a pivotal source of milk and meat. The quality of its milk and meat is predominantly dependent on the geographical location and variety of vegetation available for the diet. Camel milk (CM) is highly nutritious because of its reduced cholesterol and sugar contents along with enhanced minerals and vitamins level. The absence of beta-lactoglobulin (like human milk), makes CM a safer alternative for infants and children having Cow Milk Allergy (CMA). In addition to this, it has a unique probiotic profile both in raw and fermented form. Number of Lactic acid bacteria (LAB) including lactococcus, lactobacillus, enterococcus, streptococcus, weissella, pediococcus and many other bacteria have been detected. From these LAB Lactobacilli, Bifidobacterium and Enterococcus are widely used commercially for fermentation purpose. CM has high therapeutic value as its effectiveness is known against various ailments like fever, arthritis, asthma, gastritis, hepatitis, Jaundice, constipation, postpartum care of women, anti-venom, dropsy etc. It also has anti-diabetic, anti-microbial, antitumor potential along with its robust efficacy in the treatment of auto-immune disorders. Recently, the role of CM has been explored in brain-gut axis for the therapeutics of neurodevelopmental disorders. In this connection, a lot of grey area was available to explore the probiotics and therapeutics latent in the CM available in Pakistan. Thus, current study was designed to explore the predominant probiotic flora and antimicrobial potential of CM from different local breeds of Pakistan. The probiotics have been identified through biochemical, physiological and ribo-typing methods. In addition to this, bacteriocins (antimicrobial-agents) were screened through PCR-based approach. Results of this study revealed that CM from different breeds of camel depicted a number of similar probiotic candidates along with the range of limited variability. However, the nucleotide sequence analysis of selected anti-listerial bacteriocins exposed least variability. As a conclusion, the CM has sufficient probiotic availability and significant anti-microbial potential.

Keywords: bacteriocins, camel milk, probiotics potential, therapeutics

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Authors: Afshin Farahbakhsh, Hoda Khodadadi

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In this paper, we compare five methods of biological fuel cell fabrication by combining a Shewanella oneidensis microbial anode and a laccase-modified air-breathing cathode. As a result of biofuel cell laccase with graphite nanofibers, carbon surface (PAMAN) on the pt/hpg electrode, graphite sheets MWCNT and with (PG) and (MWCNT) showed, respectively. Describes methods for creating controllable and reproducible bio-anodes and demonstrates the versatility of hybrid biological fuel cells. The laccase-based biocathodes prepared either with the crude extract or with the purified enzyme can provide electrochemically active and stable biomaterials. The laccase-based biocathodes prepared either with the crude extract or with the purified enzyme can provide electrochemically active and stable biomaterials. When the device was fed with transdermal extracts, containing only 30μM of glucose, the average peak power was proportionally lower (0.004mW). The result of biofuel cell with graphite nanofibers showed the enzymatic fuel cell reaches 0.5 V at open circuit voltage with both, ethanol and methanol and the maximum current density observed for E2electrode was 228.94mAcm.

Keywords: enzymatic electrode, fuel cell, immobilization, laccase

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Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

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This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

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Authors: K. Karapetyan, F. Tkhruni, A. Aghajanyan, T. S. Balabekyan, L. Arstamyan

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Introduction: Globalization of the food supply has created the conditions favorable for the emergence and spread of food-borne and especially dangerous pathogens (EDP) in developing countries. The fresh-cut fruit and vegetable industry is searching for alternatives to replace chemical treatments with biopreservative approaches that ensure the safety of the processed foods product. Antimicrobial compounds of lactic acid bacteria (LAB) possess bactericidal or bacteriostatic activity against intestinal pathogens, spoilage organisms and food-borne pathogens such as Listeria monocytogenes, Staphylococcus aureus and Salmonella. Endemic strains of LAB were isolated. The strains, showing broad spectrum of antimicrobial activity against food spoiling microorganisms, were selected. The genotyping by 16S rRNA sequencing, GS-PCR, RAPD PCR methods showed that they were presented by Lactobacillus rhamnosus109, L.plantarum 65, L.plantarum 66 and Enterococcus faecium 64 species. LAB are deposited in "Microbial Depository Center" (MDC) SPC "Armbiotechnology". Methods: LAB strains were isolated from different dairy products from rural households from the highland regions of Armenia. Serially diluted samples were spread on MRS (Merck, Germany) and hydrolyzed milk agar (1,2 % w/v). Single colonies from each LAB were individually inoculated in liquid MRS medium and incubated at 37oC for 24 hours. Culture broth with biomass was centrifuged at 10,000 g during 20 min for obtaining of cell free culture broth (CFC). The antimicrobial substances from CFC broth were purified by the combination of adsorption-desorption and ion-exchange chromatography methods. Separation of bacteriocins was performed using a HPLC method on "Avex ODS" C18 column. Mass analysis of peptides recorded on the device API 4000 in the electron ionization mode. The spot-on-lawn method on the test culture plated in the solid medium was applied. The antimicrobial activity is expressed in arbitrary units (AU/ml). Results. Purification of CFC broth of LAB allowed to obtain partially purified antimicrobial preparations which contains bacteriocins with broad spectrum of antimicrobial activity. Investigation of their main biochemical properties shown, that inhibitory activity of preparations is partially reduced after treatment with proteinase K, trypsin, pepsin, suggesting a proteinaceous nature of bacteriocin-like substances containing in CFC broth. Preparations preserved their activity after heat treatment (50-121 oC, 20 min) and were stable in the pH range 3–8. The results of SDS PAAG electrophoresis show that L.plantarum 66 and Ent.faecium 64 strains have one bacteriocin (BCN) with maximal antimicrobial activity with approximate molecular weight 2.0-3.0 kDa. From L.rhamnosus 109 two BCNs were obtained. Mass spectral analysis indicates that these bacteriocins have peptide bonds and molecular weight of BCN 1 and BCN 2 are approximately 1.5 kDa and 700 Da. Discussion: Thus, our experimental data shown, that isolated endemic strains of LAB are able to produce bacteriocins with high and different inhibitory activity against broad spectrum of microorganisms of different taxonomic group, such as Salmonella sp., Esherichia coli, Bacillus sp., L.monocytogenes, Proteus mirabilis, Staph. aureus, Ps. aeruginosa. Obtained results proved the perspectives for use of endemic strains in the preservation of foodstuffs. Acknowledgments: This work was realized with financial support of the Project Global Initiatives for Preliferation Prevention (GIPP) T2- 298, ISTC A-1866.

Keywords: antimicrobial activity, bacteriocins, endemic strains, food safety

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Authors: Ameur Soukaina, Zeroual Abdellah, Mazoir Noureddine

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Molecular Electron Density Theory (MEDT) elucidates the regioselectivity of the [4+2] cycloaddition reaction between 3-aroylpyrrolo[1,2-α]quinoxaline-1,2,4(5H)-trione and butyl vinyl ether Regioselectivity and stereoselectivity. The regioselectivity mechanisms of these reactions were investigated by evaluating potential energy surfaces calculated for cycloaddition processes and DFT density-based reactivity indices. These methods have been successfully applied to predict preferred regioisomers for different method alternatives. Reactions were monitored by performing transition state optimizations, calculations of intrinsic reaction coordinates, and activation energies. The observed regioselectivity was rationalized using DFT-based reactivity descriptors such as the Parr function. Solvent effects were also investigated in 1,4-dioxane solvent using a field model for self-consistent reactions. The results were compared with experimental data to find good agreement.

Keywords: cycloaddition, DFT, ELF, MEDT, parr, stereoselectivité

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

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Authors: Salma M. Wakil

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Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

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Authors: V. Shapaval, N. K. Afseth, D. Tzimorotas, A. Kohler

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Globally there is a dramatic increase in the demand for food, energy, materials and clean water since natural resources are limited. As a result, industries are looking for ways to reduce rest materials and to improve resource efficiency. Microorganisms have a high potential to be used as bio factories for the production of primary and secondary metabolites that represent high-value bio-products (enzymes, polyunsaturated fatty acids, bio-plastics, glucans, etc.). In order to find good microbial producers, to design suitable substrates from food rest materials and to optimize fermentation conditions, rapid analytical techniques for quantifying target bio products in microbial cells are needed. In the EU project FUST (R4SME, Fp7), we have developed a fully automated high-throughput FUST system based on micro-cultivation and FTIR spectroscopy that facilitates the screening of microorganisms, substrates and fermentation conditions for the optimization of the production of different high-value metabolites (single cell oils, bio plastics). The automated system allows the preparation of 100 samples per hour. Currently, The FUST system is in use for screening of filamentous fungi in order to find oleaginous strains with the ability to produce polyunsaturated fatty acids, and the optimization of cheap substrates, derived from food rest materials, and the optimization of fermentation conditions for the high yield of single cell oil.

Keywords: FTIR spectroscopy, FUST system, screening, biotechnology

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Authors: Sajjad Seifoori

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Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: impact, molecular dynamic, graphene, spring mass

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Authors: Temitope D. Awobusuyi, Eric O. Amonsou, Muthulisi Siwela, Oluwatosin A. Ijabadeniyi

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Provitamin A-biofortified maize has been developed to alleviate Vitamin A deficiency; a major public health problem in developing countries. Amahewu, a non-alcoholic fermented maize based beverage is produced using white maize, which is deficient in Vitamin A. In this study, the suitable processing conditions for the production of amahewu using provitamin A-biofortified maize and the microbial quality of the processed products were evaluated. Provitamin A-biofortified amahewu was produced with reference to traditional processing method. Processing variables were Inoculum types (Malted provitamin A maize, Wheat bran, and lactobacillus mixed starter culture with either malted provitamin A or wheat bran) and concentration (0.5 %, 1 % and 2 %). A total of four provitamin A-biofortified amahewu products after fermentation were subjected to different storage conditions: 4ᴼC, 25ᴼC and 37ᴼC. pH and TTA were monitored throughout the storage period. Sample of provitamin A-biofortified amahewu were plated and observed every day for 5 days to assess the presence of Aerobic and Anaerobic spore formers, E.coli, Lactobacillus and Mould. The addition of starter culture substantially reduced the fermentation time (6 hour, pH 3.3) compared to those with no addition of starter culture (24 hour pH 3.5). It was observed that Lactobacillus were present from day 0 for all the storage temperatures. The presence of aerobic spore former and mould were observed on day 3. E.coli and Anaerobic spore formers were not present throughout the storage period. These microbial growth were minimal at 4ᴼC while 25ᴼC had higher counts of growth with 37ᴼC having the highest colony count. Throughout the storage period, pH of provitamin A-biofortified amahewu was stable. Provitamin A-biofortified amahewu stored under refrigerated condition (4ᴼC) had better storability compared to 25ᴼC and 37ᴼC. The production and microbial quality of provitamin A-biofortified amahewu might be important in combating Vitamin A Deficiency.

Keywords: biofortification, fermentation, maize, vitamin A deficiency

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Authors: Abdela Bulbula

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Background: Marek’s disease virus is a devastating infection, causing high morbidity and mortality in chickens in Ethiopia. Methods: The current study was conducted from March to November, 2021 with the general objective of performing antemortem and postmortem, isolation, and molecular detection of Marek’s disease virus from outbreak cases in southwestern Ethiopia. Accordingly, based on outbreak information reported from the study sites namely, Bedelle, Yayo, and Bonga towns in southwestern Ethiopia, 50 sick chickens were sampled. The backyard and intensive farming systems of chickens were included in the sampling and priorities were given for chickens that showed clinical signs that are characteristics of Marek’s disease. Results: By clinical examinations, paralysis of legs and wings, gray eye, loss of weight, difficulty in breathing, and depression were recorded on all chickens sampled for this study and death of diseased chickens was observed. In addition, enlargement of the spleen and gross lesions of the liver and heart were recorded during postmortem examination. The death of infected chickens was observed in both vaccinated and non-vaccinated flocks. Out of 50 pooled feather follicle samples, Marek’s disease virus was isolated from 14/50 (28%) by cell culture method and out of six tissue samples, the virus was isolated from 5/6(83.30%). By Real time polymerization chain reaction technique, which was targeted to detect the Meq gene, Marek’s disease virus was detected from 18/50 feather follicles which accounts for 36% of sampled chickens. Conclusion: In general, the current study showed that the circulating Marek’s disease virus in southwestern Ethiopia was caused by the oncogenic Gallid herpesvirus-2 (Serotype-1). Further research on molecular characterization of revolving virus in current and other regions is recommended for effective control of the disease through vaccination.

Keywords: Ethioi, Marek's disease, isolation, molecular

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Authors: Afsheen Aman, Shah Ali Ul Qader

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Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

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Authors: Anubha Kaushik, Raman Preet

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Distillery wastewater in the form of spent wash is a complex and strong industrial effluent, with high load of organic pollutants that may deplete dissolved oxygen on being discharged into aquatic systems and contaminate groundwater by leaching of pollutants, while untreated spent wash disposed on land acidifies the soil. Stringent legislative measures have therefore been framed in different countries for discharge standards of distillery effluent. Utilising the organic pollutants present in various types of wastes as food by mixed microbial populations is emerging as an eco-friendly approach in the recent years, in which complex organic matter is converted into simpler forms, and simultaneously useful gases are produced as renewable and clean energy sources. In the present study, wastewater from a rice bran based distillery has been used as the substrate in a dark fermenter, and native microbial consortium from the digester sludge has been used as the inoculum to treat the wastewater and produce hydrogen. After optimising the operational conditions in batch reactors, sequential batch mode and continuous flow stirred tank reactors were used to study the best operational conditions for enhanced and sustained hydrogen production and removal of pollutants. Since the rate of hydrogen production by the microbial consortium during dark fermentation is influenced by concentration of organic matter, pH and temperature, these operational conditions were optimised in batch mode studies. Maximum hydrogen production rate (347.87ml/L/d) was attained in 32h dark fermentation while a good proportion of COD also got removed from the wastewater. Slightly acidic initial pH seemed to favor biohydrogen production. In continuous stirred tank reactor, high H₂ production from distillery wastewater was obtained from a relatively shorter substrate retention time (SRT) of 48h and a moderate organic loading rate (OLR) of 172 g/l/d COD.

Keywords: distillery wastewater, hydrogen, microbial consortium, organic pollution, sludge

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