Search results for: protein isolates

Authors: A. Cheriguene, F. Chougrani

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A total of 153 wild lactic acid bacteria were isolated from goat’s milk collected from different areas in Western Algeria. The strains were identified using phenotypical, biochemical and physiological properties. API system and SDS-PAGE technique was also used in identification of the strains. Six genera were found Enterococcus (41.83%), Lactobacillus (29.40%), Lactococcus (19.60%), Leuconostoc (4.57%), Streptococcus thermophilus (3.26%) and Pediococcus (1.30%). The most abundant species were Enterococcus faecium (24 isolates), Enterococcus durans (22 isolates), Lactococcus lactis subsp. lactis (25 isolates), Lactobacillus rhamnosus (09 isolates) and Lactobacillus delbrueckii subsp. bulgaricus (07 isolates). The strains were screened for production and technological properties such as acid production, aminopeptidase activity, autolytic properties, antimicrobial activity and exopolysaccharide production. In general most tested isolates showed a good biomass separation when collected by centrifugation; as for the production of the lactic acid, results revealed that our strains are weakly acidifying; nevertheless, lactococci showed a best acidifying activity compared to lactobacilli. Aminopeptidase activity was also weak in most strains; but, it was generally higher for lactobacilli compared to lactococci, where we recorded 30 units for Lactobacillus delbrueckii subsp. bulgaricus M14. Autolytic activity was generally higher for most strains, more particularly lactobacilli where we recorded values of 71.13% and 70% of autolysis rate respectively in Lactobacillus rhamnosus strains 9S10 and 9S7. Antimicrobial activity was detected in 50% of the isolates, particularly in lactobacilli where 80% of strains tested were able to inhibit the growth of other strains. Two strains could produce exopolysaccharides, E. faecium 8M6 and E. durans 7S8. Some strains were able to maintain two or three technological characteristics together.

Keywords: lactic acid bacteria, technological properties, acidification, aminopeptidase acivity (AP), autolysis

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Authors: Mehrnaz Aminifar

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The relation between textural parameters and casein network on release of aromatic compounds was investigated over 90-days of ripening. Low DE maltodextrin and WPI were used to modify the textural properties of low fat brined cheese. Hardness, brittleness and compaction of casein network were affected by addition of maltodextrin and WPI. Textural properties and aroma release from cheese texture were affected by interaction of WPI protein-cheese protein and maltodexterin-cheese protein.

Keywords: aroma release, brined cheese, maltodexterin, WPI

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Authors: Phanwipa Pangsri, Yawariyah Weahayee

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The lactic acid bacteria (LAB) were isolated from 10 samples of fermented foods (Sa-tor-dong and Bodo) in South locality of Thailand. The 23 isolates of lactic acid bacteria were selected, which were exhibited a clear zone and growth on MRS agar supplemented with CaCO3. All of lactic acid bacteria were tested on morphological and biochemical. The result showed that all isolates were Gram’s positive, non-spore forming but only 10 isolates displayed catalase negative. The 10 isolates including BD 1.1, BD 1.2, BD 2.1, BD2.2, BD 2.3, BD 3.1, BD 4.1, BD 5.2, ST4.1, and ST 5.2 were selected for inhibition activity determination. Only 2 strains (ST 4.1 and BD 2.3) showed inhibition zone on agar, when using Escherichia coli sp. as target strain. The ST 4.1 showed highest inhibition zone on agar, which was selected for probiotic property testing. The ST4.1 isolate could grow in MRS broth containing a high concentration of sodium chloride 6%, bile salts 7%, pH 4-10 and vary temperature at 15-45^oC.

Keywords: lactic acid bacteria, probiotic, antimicrobial, probiotic property testing

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Authors: Zahid Rehman, TorOve Leiknes

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Quorum sensing (QS) is the process by which bacteria communicate with each other through small signaling molecules, such as N-acylhomoserine lactones (AHLs). Also, certain bacteria have the ability to degrade AHL molecules by a process referred to as quorum quenching (QQ); therefore, QQ can be used to control bacterial infections and biofilm formation. In this study, we aimed to identify new species of bacteria with QQ activities. To achieve this, sediments from Red Sea were collected either in the close vicinity of Sea grass or from area with no vegetation. From these samples, we isolated 72 bacterial strains and tested their ability to degrade/inactivate AHL molecules. Chromobacterium violaceum based bioassay was used in initial screening of isolates for QQ activity. The QQ activity of the positive isolates was further confirmed and quantified by employing liquid chromatography and mass spectrometry. These analyses showed that isolated bacterial strain could degrade AHL molecules with different acyl chain length and modifications. Sequencing of 16S-rRNA genes of positive isolates revealed that they belong to three different genera. Specifically, two isolates belong to genus Erythrobacter, four to Labrenzia and one isolate belongs to Bacterioplanes. Time course experiment showed that isolate belonging to genus Erythrobacter could degrade AHLs faster than other isolates. Furthermore, these isolates were tested for their ability to inhibit formation of biofilm and degradation of 3OXO-C12 AHLs produced by P. aeruginosa PAO1. Our results showed that isolate VG12 is better at controlling biofilm formation. This aligns with the ability of VG12 to cause at least 10-fold reduction in the amount of different AHLs tested.

Keywords: quorum sensing, biofilm, quorum quenching, anti-biofouling

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Authors: C. E. Chinma, S. O. Azeez, J. C. Anuonye, O. B. Ocheme, C. M. Yakubu, S. James, E. U. Ohuoba, I. A. Baba

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There is growing interest in the use of rice bran protein in food formulation due to its hypoallergenic protein, high nutritional value and health promoting potentials. For the first time, the amino acid profile, protein digestibility, antioxidant, and functional properties of protein concentrate from some local varieties of rice bran from Nigeria were studied for possible food applications. Protein concentrates were prepared from rice bran and analysed using standard methods. Results showed that protein content of Kwandala, Yardass, Jeep, and Jamila were 69.24%, 69.97%, 68.73%, and 71.62%, respectively while total essential amino acid were 52.71, 53.03, 51.86, and 55.75g/100g protein, respectively. In vitro protein digestibility of protein concentrate from Kwandala, Yardass, Jeep and Jamila were 90.70%, 91.39%, 90.57% and 91.63% respectively. DPPH radical inhibition of protein from Kwandala, Yardass, Jeep, and Jamila were 48.15%, 48.90%, 47.56%, and 53.29%, respectively while ferric reducing ability power were 0.52, 0.55, 0.47 and 0.67mmol TE per gram, respectively. Protein concentrate from Jamila had higher onset (92.57oC) and denaturation temperature (102.13oC), and enthalpy (0.72J/g) than Jeep (91.46oC, 101.76oC, and 0.68J/g, respectively), Kwandala (90.32oC, 100.54oC and 0.57J/g, respectively), and Yardass (88.94oC, 99.45oC, and 0.51J/g, respectively). In vitro digestibility of protein from Kwandala, Yardas, Jeep, and Jamila were 90.70%, 91.39%, 90.57% and 91.63% respectively. Oil absorption capacity of Kwandala, Yardass, Jeep, and Jamila were 3.61, 3.73, 3.40, and 4.23g oil/g sample respectively, while water absorption capacity were 4.19, 4.32, 3.55 and 4.48g water/g sample, respectively. Protein concentrates had low bulk density (0.37-0.43g/ml). Protein concentrate from Jamila rice bran had the highest foam capacity (37.25%), followed by Yardass (34.20%), Kwandala (30.14%) and Jeep (28.90%). Protein concentrates showed low emulsifying and gelling capacities. In conclusion, protein concentrate prepared from these local rice bran varieties could serve as functional ingredients in food formulations and for enriching low protein foods.

Keywords: rice bran protein, amino acid profile, protein digestibility, antioxidant and functional properties

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Authors: Prajna Metta, Yanti Rusyanti, Nunung Rusminah, Bremmy Laksono

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The decrease of neutrophil chemotaxis function may cause increased susceptibility to aggressive periodontitis (AP). Neutrophil chemotaxis is affected by formyl peptide receptor 1 (FPR1), which when activated will respond to bacterial chemotactic peptide formyl methionyl leusyl phenylalanine (FMLP). FPR1 protein value is decreased in response to a wide number of inflammatory stimuli in AP patients. This study was aimed to assess the alteration of FPR1 protein value in AP patients and if FPR1 protein value could be used as an indicator of neutrophil chemotaxis dysfunction in AP. This is a case control study with 20 AP patients and 20 control subjects. Three milliliters of peripheral blood were drawn and analyzed for FPR1 protein value with ELISA. The data were statistically analyzed with Mann-Whitney test (p>0,05). Results showed that the mean value of FPR1 protein value in AP group is 0,353 pg/mL (0,11 to 1,18 pg/mL) and the mean value of FPR1 protein value in control group is 0,296 pg/mL (0,05 to 0,88 pg/mL). P value 0,787 > 0,05 suggested that there is no significant difference of FPR1 protein value in both groups. The present study suggests that FPR1 protein value has no significance alteration in AP patients and could not be used as an indicator of neutrophil chemotaxis dysfunction.

Keywords: aggressive periodontitis, chemotaxis dysfunction, FPR1 protein value, neutrophil

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Authors: Phakamas Rachamontree, Theerawut Phusantisampan, Natthakorn Woravutthikul, Peerapong Pornwongthong, Malinee Sriariyanun

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A total of 115 yeast strains isolated from local cassava processing wastes were measured for crude protein content. Among these strains, the strain MSY-2 possessed the highest protein concentration (>3.5 mg protein/mL). By using molecular identification tools, it was identified to be a strain of Pichia kudriavzevii based on similarity of D1/D2 domain of 26S rDNA region. In this study, to optimize the protein production by MSY-2 strain, Response Surface Methodology (RSM) was applied. The tested parameters were the carbon content, nitrogen content, and incubation time. Here, the value of regression coefficient (R2) = 0.7194 could be explained by the model, which is high to support the significance of the model. Under the optimal condition, the protein content was produced up to 3.77 g per L of the culture and MSY-2 strain contain 66.8 g protein per 100 g of cell dry weight. These results revealed the plausibility of applying the novel strain of yeast in single-cell protein production.

Keywords: single cell protein, response surface methodology, yeast, cassava processing waste

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Authors: Nuha Mansour Alhazmi, Magda Mohamed Aly, Fardus M. Bokhari, Ahmed Bahieldin, Sherif Edris

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Out of 30 fungal isolates, 2 new isolates were proven to degrade poly-β-hydroxybutyrate (PHB). Enzyme assay for these isolates indicated the optimal environmental conditions required for depolymerase enzyme to induce the highest level of biopolymer degradation. The two isolates were basically characterized at the morphological level as Trichoderma asperellum (isolate S1), and Aspergillus fumigates (isolate S2) using standard approaches. The aim of the present study was to characterize these two isolates at the molecular level based on the highly diverged rRNA gene(s). Within this gene, two domains of the ribosome large subunit (LSU) namely internal transcribed spacer (ITS) and 26S were utilized in the analysis. The first domain comprises the ITS1/5.8S/ITS2 regions ( > 500 bp), while the second domain comprises the D1/D2/D3 regions ( > 1200 bp). Sanger sequencing was conducted at Macrogen (Inc.) for the two isolates using primers ITS1/ITS4 for the first domain, while primers LROR/LR7 for the second domain. Sizes of the first domain ranged between 594-602 bp for S1 isolate and 581-594 bp for S2 isolate, while those of the second domain ranged between 1228-1238 bp for S1 isolate and 1156-1291 for S2 isolate. BLAST analysis indicated 99% identities of the first domain of S1 isolate with T. asperellum isolates XP22 (ID: KX664456.1), CTCCSJ-G-HB40564 (ID: KY750349.1), CTCCSJ-F-ZY40590 (ID: KY750362.1) and TV (ID: KU341015.1). BLAST of the first domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other T. asperellum and A. fumigatus isolates and strains showed high level of identities with S1 and S2 isolates, respectively, based on the diversity of the first domain. BLAST of the second domain of S1 isolate indicated 99 and 100% identities with only two strains of T. asperellum namely TR 3 (ID: HM466685.1) and G (ID: KF723005.1), respectively. However, other T. species (ex., atroviride, hamatum, deliquescens, harzianum, etc.) also showed high level of identities. BLAST of the second domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other A. fumigatus isolates and strains showed high level of identities with S2 isolate. Overall, the results of molecular characterization based on rRNA diversity for the two isolates of T. asperellum and A. fumigatus matched those obtained by morphological characterization. In addition, ITS domain proved to be more sensitive than 26S domain in diversity profiling of fungi at the species level.

Keywords: Aspergillus fumigates, Trichoderma asperellum, PHB, degradation, BLAST, ITS, 26S, rRNA

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Authors: Seyed Mohammad Hosein Al Omrani Nejad, Ali Rezvani Aghdam

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This study was done in order to evaluation different irrigation intervals on amount of protein, and gel production in Aloe vera, a traditional medicinal plant. Plants was plnted in Greenhouse and irrigated according to Accumulative Pan Evaporation(APE). The treatments were included 20, 40, 60, 80, 100, 120, 140, 160, 180, and 200 mm APE which has been showed W1,W2, W3, W4, W5, W6, W7, W8,W9 and W10 respectively.The amount of protein and gel production was measured seperately. Results showed that highest protein and fresh weight of gel obtained plants which irrigated W6 and W7 respectively. According to these results can recomend which if plant irrigatedwhen APE reached 120 and 140 mm by Class A Evaporation Pan method gel production and protein would besuitable in north of khozestan province in limited irrigation conditions.

Keywords: irrigation, protein, gel, aloe vera, Iran

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Authors: Muna Jalal Ali, Essam A. Makky, Mashitah M. Yusoff

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Objectives: The aim of this study to evaluate the antimicrobial susceptibility of combined toothpaste with medicinal plants and the relations between the commercial toothpaste to its price and the patient age as well. Materials and Methods: Oral isolates of different patients aged 3 to 60 years were obtained, purified, and tested against four different ethnomedicinal plant extracts for antimicrobial activity. A total of 10 different commercial toothpastes (different brands and prices) were collected from the market, and the combined action of the medicinal plants and toothpaste was studied. Results: We found a higher bacterial population in the age group of 3–40 years than the group of 40–60 years, with approximately 44% and 32%, respectively. The combined action of ethanolic extract (alone) against oral isolates showed a synergistic effect, with 32.20, 30.50, and 25.42% for combinations A (Ci/Ca), B (Ci/Ca/P), and C (Ci/Ca/P/N), respectively. By contrast, the combined action of ethnomedicinal plants with 10 different toothpastes improved the antimicrobial sensitivity by 60, 100, and 0% for combinations A, B, and C respectively. Clinical relevance: The ethanolic extract of only combinations A and B with commercial toothpaste showed high antibacterial activity against oral isolates and the effectiveness of toothpaste is not related to the price.

Keywords: microbial evolution, oral isolates, ethnomedicinal plants, antimicrobial activity, toothpaste

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Authors: Er-Yuan Chuang

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Bio-mimetic matters have biological functionalities. This might be valuable in the development of versatile biomaterials. At biological fields, protein-based materials might be components to form a 3D network of extracellular biomolecules, containing growth factors. Also, the protein-based biomaterial provides biochemical and structural assistance of adjacent cells. In this study, we try to prepare protein based biomaterial, which was harvested from living animal. We analyzed it’s chemical, physical and biological property in vitro. Besides, in vivo bio-interaction of the prepared biomimetic matrix was tested in an animal model. The protein-based biomaterial has degradability and biocompatibility. This development could be used for tissue regenerations and be served as platform technologies.

Keywords: protein based, in vitro study, in vivo study, biomaterials

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Authors: P. Chihomvu, P. Stegmann, M. Pillay

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Pollution of the Klip River has caused microorganisms inhabiting it to develop protective survival mechanisms. This study isolated and characterized the heavy metal resistant bacteria in the Klip River. Water and sediment samples were collected from six sites along the course of the river. The pH, turbidity, salinity, temperature and dissolved oxygen were measured in-situ. The concentrations of six heavy metals (Cd, Cu, Fe, Ni, Pb, and Zn) of the water samples were determined by atomic absorption spectroscopy. Biochemical and antibiotic profiles of the isolates were assessed using the API 20E® and Kirby Bauer Method. Growth studies were carried out using spectrophotometric methods. The isolates were identified using 16SrDNA sequencing. The uppermost part of the Klip River with the lowest pH had the highest levels of heavy metals. Turbidity, salinity and specific conductivity increased measurably at Site 4 (Henley on Klip Weir). MIC tests showed that 16 isolates exhibited high iron and lead resistance. Antibiotic susceptibility tests revealed that the isolates exhibited multi-tolerances to drugs such as tetracycline, ampicillin, and amoxicillin.

Keywords: Klip River, heavy metals, resistance, 16SrDNA

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Authors: A. Zh. Aupova, A. Ulankyzy, A. Sarsenova, A. Kussayin, Sh. Turarbek, N. Moldagulova, A. Kurmanbayev

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One of the methods of organic waste bioconversion into environmentally-friendly fertilizer is composting. Microorganisms that produce hydrolytic enzymes play a significant role in accelerating the process of organic waste composting. We studied the enzymatic potential (amylase, protease, cellulase, lipase, urease activity) of bacteria isolated from the sewage sludge of Nur-Sultan, Rudny, and Fort-Shevchenko cities, the dacha soil of Nur-Sultan city, and freshly cut grass from the dacha for processing organic waste and identifying active strains. Microorganism isolation was carried out by the cultures enrichment method on liquid nutrient media, followed by inoculating on different solid media to isolate individual colonies. As a result, sixty-one microorganisms were isolated, three of which were thermophiles (DS1, DS2, and DS3). The highest number of isolates, twenty-one and eighteen, were isolated from sewage sludge of Nur-Sultan and Rudny cities, respectively. Ten isolates were isolated from the wastewater of the sewage treatment plant in Fort-Shevchenko. From the dacha soil of Nur-Sultan city and freshly cut grass - 9 and 5 isolates were revealed, respectively. The lipolytic, proteolytic, amylolytic, cellulolytic, ureolytic, and oil-oxidizing activities of isolates were studied. According to the results of experiments, starch hydrolysis (amylolytic activity) was found in 2 isolates - CB2/2, and CB2/1. Three isolates - CB2, CB2/1, and CB1/1 were selected for the highest ability to break down casein. Among isolated 61 bacterial cultures, three isolates could break down fats - CB3, CBG1/1, and IL3. Seven strains had cellulolytic activity - DS1, DS2, IL3, IL5, P2, P5, and P3. Six isolates rapidly decomposed urea. Isolate P1 could break down casein and cellulose. Isolate DS3 was a thermophile and had cellulolytic activity. Thus, based on the conducted studies, 15 isolates were selected as a potential for sewage sludge composting - CB2, CB3, CB1/1, CB2/2, CBG1/1, CB2/1, DS1, DS2, DS3, IL3, IL5, P1, P2, P5, P3. Selected strains were identified on a mass spectrometer (Maldi-TOF). The isolate - CB 3 was referred to the genus Rhodococcus rhodochrous; two isolates CB2 and CB1 / 1 - to Bacillus cereus, CB 2/2 - to Cryseobacterium arachidis, CBG 1/1 - to Pseudoxanthomonas sp., CB2/1 - to Bacillus megaterium, DS1 - to Pediococcus acidilactici, DS2 - to Paenibacillus residui, DS3 - to Brevibacillus invocatus, three strains IL3, P5, P3 - to Enterobacter cloacae, two strains IL5, P2 - to Ochrobactrum intermedium, and P1 - Bacillus lichenoformis. Hence, 60 isolates were isolated from the wastewater of the cities of Nur-Sultan, Rudny, Fort-Shevchenko, the dacha soil of Nur-Sultan city, and freshly cut grass from the dacha. Based on the highest enzymatic activity, 15 active isolates were selected and identified. These strains may become the candidates for bio preparation for sewage sludge processing.

Keywords: sewage sludge, composting, bacteria, enzymatic activity

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Authors: Shayli Varasteh Moradi, Wayne A. Johnston, Dejan Gagoski, Kirill Alexandrov

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The demand for a rapid and more efficient technique to identify protein-protein interaction particularly in the areas of therapeutics and diagnostics development is growing. The method described here is a rapid in vitro protein-protein interaction analysis approach based on AlphaLISA technology combined with Leishmania tarentolae cell-free protein production (LTE) system. Cell-free protein synthesis allows the rapid production of recombinant proteins in a multiplexed format. Among available in vitro expression systems, LTE offers several advantages over other eukaryotic cell-free systems. It is based on a fast growing fermentable organism that is inexpensive in cultivation and lysate production. High integrity of proteins produced in this system and the ability to co-express multiple proteins makes it a desirable method for screening protein interactions. Following the translation of protein pairs in LTE system, the physical interaction between proteins of interests is analysed by AlphaLISA assay. The assay is performed using unpurified in vitro translation reaction and therefore can be readily multiplexed. This approach can be used in various research applications such as epitope mapping, antigen-antibody analysis and protein interaction network mapping. The intra-viral protein interaction network of Zika virus was studied using the developed technique. The viral proteins were co-expressed pair-wise in LTE and all possible interactions among viral proteins were tested using AlphaLISA. The assay resulted to the identification of 54 intra-viral protein-protein interactions from which 19 binary interactions were found to be novel. The presented technique provides a powerful tool for rapid analysis of protein-protein interaction with high sensitivity and throughput.

Keywords: AlphaLISA technology, cell-free protein expression, epitope mapping, Leishmania tarentolae, protein-protein interaction

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Authors: Sonaal Ramsookmohan

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Legume seeds are common foods in human diet and have been identied as a valuable source of human nutritonn Since they are useful sources of protein; legume proteins are used in many food applicatonsn Critcal functonal propertes are recognized to impact the quality of foodn Cowpea (Vigna unguiculata), has been well documented for its immense potental in contributng to food security forming part of daily staple diets in most developing countriesn. In this study, cowpea seeds were used to prepare cowpea four, protein isolates by the salt extractonndialysis method and peptdes by enzymatc hydrolysis using Alcalase and Flavourzymen Functonal analyses such as water absorpton capacity, oil absorpton capacity, emulsifying and foaming propertes were conducted on the cowpea peptdesn The physicochemical propertes determine their potental applicaton in food industries as functonal ingredientsn Cowpea peptdes could increase the value of cowpea by expanding its use, as well as contribute to the legume grain sector.

Keywords: physicochemical, peptides, Cowpea, alcalase, flavourzyme

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Authors: Sharon K. Mahlangu, Mustapha Mohammed, Felix D. Dakora

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Rural households in Africa depend largely on legumes as a source of high-protein food due to N₂-fixation by rhizobia when they infect plant roots. However, the legume/rhizobia symbiosis can exhibit some level of specificity such that some legumes may be selectively nodulated by only a particular group of rhizobia. In contrast, some legumes are highly promiscuous and are nodulated by a wide range of rhizobia. Little is known about the nodulation promiscuity of bacterial symbionts from wild legumes such as Aspalathus linearis, especially if they can nodulate cultivated grain legumes such as cowpea and Kersting’s groundnut. Determining the host range of the symbionts of wild legumes can potentially reveal novel rhizobial strains that can be used to increase nitrogen fixation in cultivated legumes. In this study, bacteria were isolated and tested for their ability to induce root nodules on their homologous hosts. Seeds were surface-sterilized with alcohol and sodium hypochlorite and planted in sterile sand contained in plastic pots. The pot surface was covered with sterile non-absorbent cotton wool to avoid contamination. The plants were watered with nitrogen-free nutrient solution and sterile water in alternation. Three replicate pots were used per isolate. The plants were grown for 90 days in a naturally-lit glasshouse and assessed for nodulation (nodule number and nodule biomass) and shoot biomass. Seven isolates from each of Kersting’s groundnut and cowpea and two from Rooibos tea plants were tested for their ability to nodulate soybean, mung bean, common bean and Bambara groundnut. The results showed that of the isolates from cowpea, where VUSA55 and VUSA42 could nodulate all test host plants, followed by VUSA48 which nodulated cowpea, Bambara groundnut and soybean. The two isolates from Rooibos tea plants nodulated Bambara groundnut, soybean and common bean. However, isolate L1R3.3.1 also nodulated mung bean. There was a greater accumulation of shoot biomass when cowpea isolate VUSA55 nodulated common bean. Isolate VUSA55 produced the highest shoot biomass, followed by VUSA42 and VUSA48. The two Kersting’s groundnut isolates, MGSA131 and MGSA110, accumulated average shoot biomass. In contrast, the two Rooibos tea isolates induced a higher accumulation of biomass in Bambara groundnut, followed by common bean. The results suggest that inoculating these agriculturally important grain legumes with cowpea isolates can contribute to improved soil fertility, especially soil nitrogen levels.

Keywords: legumes, nitrogen fixation, nodulation, rhizobia

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Authors: Lillian Musila, Valerie Oundo, Daniel Erwin, Willie Sang

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Staphylococcus aureus infections are a major cause of nosocomial infections in Kenya. Methicillin resistant S. aureus (MRSA) infections are a significant burden to public health and are associated with considerable morbidity and mortality. At a hospital in Western Kenya two clusters of MRSA cases emerged within short periods of time. In this study we explored whether these clusters represented a nosocomial outbreak by characterizing the isolates using phenotypic and molecular assays and examining epidemiological data to identify possible transmission patterns. Specimens from the site of infection of the subjects were collected, cultured and S. aureus isolates identified phenotypically and confirmed by APIStaph™. MRSA were identified by cefoxitin disk screening per CLSI guidelines. MRSA were further characterized based on their antibiotic susceptibility patterns and spa gene typing. Characteristics of cases with MRSA isolates were compared with those with MSSA isolated around the same time period. Two cases of MRSA infection were identified in the two week period between 21 April and 4 May 2015. A further 2 MRSA isolates were identified on the same day on 7 September 2015. The antibiotic resistance patterns of the two MRSA isolates in the 1st cluster of cases were different suggesting that these were distinct isolates. One isolate had spa type t2029 and the other had a novel spa type. The 2 isolates were obtained from urine and an open skin wound. In the 2nd cluster of MRSA isolates, the antibiotic susceptibility patterns were similar but isolates had different spa types: one was t037 and the other a novel spa type different from the novel MRSA spa type in the first cluster. Both cases in the second cluster were admitted into the hospital but one infection was community- and the other hospital-acquired. Only one of the four MRSA cases was classified as an HAI from an infection acquired post-operatively. When compared to other S. aureus strains isolated within the same time period from the same hospital only one spa type t2029 was found in both MRSA and non-MRSA strains. None of the cases infected with MRSA in the two clusters shared any common epidemiological characteristic such as age, sex or known risk factors for MRSA such as prolonged hospitalization or institutionalization. These data suggest that the observed MRSA clusters were multi strain clusters and not an outbreak of a single strain. There was no clear relationship between the isolates by spa type suggesting that no transmission was occurring within the hospital between these cluster cases but rather that the majority of the MRSA strains were circulating in the community. There was high diversity of spa types among the MRSA strains with none of the isolates sharing spa types. Identification of disease clusters in space and time is critical for immediate infection control action and patient management. Spa gene typing is a rapid way of confirming or ruling out MRSA outbreaks so that costly interventions are applied only when necessary.

Keywords: cluster, Kenya, MRSA, spa typing

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Authors: Afroza Parvin, Md. Mahmudul Hasan, Md. Rokunozzaman, Papon Debnath

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The effluents of textile industries have considerable amounts of heavy metals, causing potential microbial metal loads if discharged into the environment without treatment. Aim: In this present study, both lactose and non-lactose fermenting bacterial isolates were isolated from textile industrial effluents of a specific region of Bangladesh, named Savar, to compare and understand the load of heavy metals in these microorganisms determining the effects of heavy metal resistance properties on antibiotic resistance. Methods: Five different textile industrial canals of Savar were selected, and effluent samples were collected in 2016 between June to August. Total bacterial colony (TBC) was counted for day 1 to day 5 for 10-6 dilution of samples to 10-10 dilution. All the isolates were isolated and selected using 4 differential media, and tested for the determination of minimum inhibitory concentration (MIC) of heavy metals and antibiotic susceptibility test with plate assay method and modified Kirby-Bauer disc diffusion method, respectively. To detect the combined effect of heavy metals and antibiotics, a binary exposure experiment was performed, and to understand the plasmid profiling plasmid DNA was extracted by alkaline lysis method of some selective isolates. Results: Most of the cases, the colony forming units (CFU) per plate for 50 ul diluted sample were uncountable at 10-6 dilution, however, countable for 10-10 dilution and it didn’t vary much from canal to canal. A total of 50 Shigella, 50 Salmonella, and 100 E.coli (Escherichia coli) like bacterial isolates were selected for this study where the MIC was less than or equal to 0.6 mM for 100% Shigella and Salmonella like isolates, however, only 3% E. coli like isolates had the same MIC for nickel (Ni). The MIC for chromium (Cr) was less than or equal to 2.0 mM for 16% Shigella, 20% Salmonella, and 17% E. coli like isolates. Around 60% of both Shigella and Salmonella, but only 20% of E.coli like isolates had a MIC of less than or equal to 1.2 mM for lead (Pb). The most prevalent resistant pattern for azithromycin (AZM) for Shigella and Salmonella like isolates was found 38% and 48%, respectively; however, for E.coli like isolates, the highest pattern (36%) was found for sulfamethoxazole-trimethoprim (SXT). In the binary exposure experiment, antibiotic zone of inhibition was mostly increased in the presence of heavy metals for all types of isolates. The highest sized plasmid was found 21 Kb and 14 Kb for lactose and non-lactose fermenting isolates, respectively. Conclusion: Microbial resistance to antibiotics and metal ions, has potential health hazards because these traits are generally associated with transmissible plasmids. Microorganisms resistant to antibiotics and tolerant to metals appear as a result of exposure to metal-contaminated environments.

Keywords: antibiotics, effluents, heavy metals, minimum inhibitory concentration, resistance

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: M. Raissy, M. Shahrani

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The present study was done to evaluate the presence of tetracycline resistance genes in Lactococcus garvieae isolated from cultured rainbow trout, West Iran. The isolates were examined for antimicrobial resistance using disc diffusion method. Of the 49 strains tested, 19 were resistant to tetracycline (38.7%), 32 to enrofloxacin (65.3%), 21 to erythromycin (42.8%), 20 to chloramphenicol and trimetoprim-sulfamethoxazole (40.8%). The strains were then characterized for their genotypic resistance profiles. The results revealed that all 49 isolates contained at least one of the tetracycline resistance genes. Tet (A) was found in 89.4% of tetracycline resistant isolates and the frequency of other gene were as follow: tet (E) 42.1%, tet (B) 47.3%, tet (D) 15.7%, tet (L) 26.3%, tet (K) 52.6%, tet (G) 36.8%, tet (34) 21%, tet (S) 63.1%, tet (C) 57.8%, tet (M) 73.6%, tet (O) 42.1%. The results revealed high levels of antibiotic resistance in L. garvieae strains which is a potential danger for trout culture as well as for public health.

Keywords: Lactococcus garvieae, tetracycline resistance genes, rainbow trout, antimicrobial resistance

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Authors: Padmanabhan D, Kavitha S

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The purpose of the study is to investigate arsenic resistance ability of indigenous microflora and its ability to utilize arsenic species form containing water source. PS-6 potential arsenic tolerance bacterium was screened from thirty isolates from Pichavaram Mangroves of India having tolerance to grow up to 1000 mg/l of As (V) and 800 mg/l of As (III) and arsenic utilization ability of 98 % of As (V) and 97% of As (III) with initial concentration of 3-5 mg/l within 48 hrs. Optimum pH and temperature was found to be ~7-7.4 and 37°C. Active growth of PS-6 in minimal salt media (MSB) helps in cost effective biomass production. Dry weight analysis of PS-6 has shown significant difference in biomass when exposed to As (III) and As (V). Protein level study of PS-6 after exposing to As (V) and As (III) shown modification in total protein concentration and variation in SDS-PAGE pattern. PS-6 was identified as Bacillus licheniformis based on partially sequenced of 16S rRNA using NCBI Blast. Further investigation will help in using this potential bacterium as a well-grounded source for urgency.

Keywords: arsenite, arsenate, Bacillus licheniformis, utilization

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Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

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Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

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Authors: Mudassar Mohiuddin, Zahid Iqbal

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Introduction: Clostridium perfringens is an important pathogen responsible for causing enteric diseases in both human and animals. The bacteria produce several toxins. These toxins play vital role in the pathogenesis of various fatal enteric diseases and are classified into five types, on the basis of the differential production of Alpha, Beta, Epsilon and Iota toxins. In addition to the so-called major toxins, there are other toxins like beta2 toxin, produced by some strains of C. perfringens which may play a role in the pathogenesis of disease. Aim of the study: In this study a multiplex PCR assay was developed and used for detection of cpb2 gene to identify the Beta2 harboring isolates among different types of C. perfringens. Objectives: The primary objective of this study was to identify the prevalence of β2-toxin gene in local isolates of Clostridium perfringens. Methodology: This was an experimental study. Random sampling technique was used. A total of 97 sheep and goats were included in this study. All were Pakistani local breeds. The samples were collected during the period from Sep, 2014 to Mar, 2015 from selected districts of Punjab province (Pakistan). Faecal samples were cultured in cooked meat media. The identification of Clostridium perfringens was made on the basis of biochemical tests. Multiplex PCR was performed to identify the toxin genes. Results: A total of 43 C. perfringens isolates were genotyped using multiplex PCR assay. The gene encoding C. perfringens β2-toxin (cpb2) was present in more than 50% of the isolates genotyped. However, the prevalence of this gene varied between sheep and goat isolates. Conclusion: The present study suggests the high occurrence of C. perfringens b2-toxin (cpb2) in the local isolates of Pakistan. As β2-toxin is present in both healthy and diseased animals, so further studies are suggested to establish the role of β2-toxin in pathogenesis of the clostridial enteric diseases.

Keywords: beta 2 toxin gene, clostridium perfringens, enteric diseases, goats, multiplex PCR, sheep

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Authors: Xiao Zhou, Jianlin Cheng

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A single amino acid mutation can have a significant impact on the stability of protein structure. Thus, the prediction of protein stability change induced by single site mutations is critical and useful for studying protein function and structure. Here, we presented a deep learning network with the dropout technique for predicting protein stability changes upon single amino acid substitution. While using only protein sequence as input, the overall prediction accuracy of the method on a standard benchmark is >85%, which is higher than existing sequence-based methods and is comparable to the methods that use not only protein sequence but also tertiary structure, pH value and temperature. The results demonstrate that deep learning is a promising technique for protein stability prediction. The good performance of this sequence-based method makes it a valuable tool for predicting the impact of mutations on most proteins whose experimental structures are not available. Both the downloadable software package and the user-friendly web server (DNpro) that implement the method for predicting protein stability changes induced by amino acid mutations are freely available for the community to use.

Keywords: bioinformatics, deep learning, protein stability prediction, biological data mining

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Authors: Duygu Çimen, Nilay Bereli, Adil Denizli

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In this study is to synthesis magnetic nanoparticles for purify protein C. For this aim, N-Methacryloyl-(L)-histidine methyl ester (MAH) containing 2-hydroxyethyl methacrylate (HEMA) based magnetic nanoparticles were synthesized by using micro-emulsion polymerization technique for templating protein C via metal chelation. The obtained nanoparticles were characterized with Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), zeta-size analysis and electron spin resonance (ESR) spectroscopy. After that, they were used for protein C purification from aqueous solution to evaluate/optimize the adsorption condition. Hereby, the effecting factors such as concentration, pH, ionic strength, temperature, and reusability were evaluated. As the last step, protein C was determined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Keywords: immobilized metal affinity chromatography (IMAC), magnetic nanoparticle, protein C, hydroxyethyl methacrylate (HEMA)

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Authors: Ahmed M. Hjazi, Bader M. Hjazi

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Protein 4.1 is a crucial component of complex interactions between the cytoskeleton and other junctional complex proteins. When the gene encoding this protein is altered, resulting in reduced expression, or when the protein is absent, the red cell undergoes a significant structural change. This research aims to achieve a deeper comprehension of the biochemical effects of red cell protein deficiency. A Tandem Mass Spectrometry Analysis (TMT-MS/MS) of patient cells lacking protein 4.1 compared to three healthy controls was achieved by the Proteomics Institute of the University of Bristol. The SDS-PAGE and Western blotting were utilized on the original patient sample and controls to partially confirm TMT MS/MS data analysis of the protein-4.1-deficient cells. Compared to healthy controls, protein levels in samples lacking protein 4.1 had a significantly higher concentration of proteins that probably originated from reticulocytes. This could occur if the patient has an elevated reticulocyte count. The increase in chaperone and reticulocyte-associated proteins was most notable in this study. This may result from elevated quantities of reticulocytes in patients with hereditary elliptocytosis.

Keywords: hereditary elliptocytosis, protein 4.1, red cells, tandem mass spectrometry data.

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Authors: Yusuf Ali Abdulle, Azhar Uddin Keerio

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Background: Protein elicitors play a key role in signaling or displaying plant defense mechanisms and emerging as vital tools for bio-control of insects. This study was aimed at the characterization of the novel protein elicitor isolated from entomopathogenic fungi Lecanicillium lecanii (V3) strain and its activity against Whitefly, Bemisia tabaci in cotton. The sequence of purified elicitor protein showed 100% similarity with hypothetical protein LEL_00878 [Cordyceps confragosa RCEF 1005], GenBank no (OAA81333.1). This novel protein elicitor has 253 amino acid residues and 762bp with a molecular mass of 29 kDa. The protein recombinant was expressed in Escherichia coli using pET‐28a (+) plasmid. Effects of purified novel protein elicitor on Bemisia tabaci were determined at three concentrations of protein (i.e., 58.32, 41.22, 35.41 μg mL⁻¹) on cotton plants and were exposed to newly molted adult B.tabaci. Bioassay results showed a significant effect of the exogenous application of novel protein elicitor on B. tabaci in cotton. In addition, the gene expression analysis found a significant up-regulation of the major genes associated with salicylic acid (SA) and jasmonic acid (JA) linked plant defense pathways in elicitor protein-treated plants. Our results suggested the potential application of a novel protein elicitor derived from Lecanicillium lecanii as a future bio-intensive controlling approach against the whitefly, Bemisia tabaci.

Keywords: resistance, Lecanicillium lecanii, secondary metabolites, whitefly

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Authors: Amal Saafan, Kareem Al Sofy, Sameh AbdelGhani, Magdy Amin

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Background: Acinetobacter spp. resistance towards β-lactam antibiotics is mediated mainly by different classes of β-lactamases production; detection of some genes responsible for production of β-lactamases is the objective of the study. Methods: One hundred fifty bacterial isolates were recovered from blood, sputum, and urine specimens from different hospitals in Egypt. Sixty-nine isolate were identified as Acinetobacter baumannii using traditional biochemical tests, CHROM agar, MicroScan and PCR amplification of blaoxa-51like gene. Acinetobacterbaumannii isolates were grouped into carbapenem resistant group (GP1), cefotaxime, ceftazidime and cefoxitin resistant group (GP2) and carbapenem and cephalosporin non-resistant group (GP3). Carbapenemase activity was screened using modified Hodge test (MHT) for GP1.Metallo-β-lactamases screening was performed for MHT positive isolates using double disk synergy test (DDST) and combined disk test (CDT). Amp C activity was screened using Amp C disk test with Tris-EDTA, DDST, and CDT for GP2. Finally, PCR amplification of blaoxa-51like, blaoxa-23like, blaIMP-like, blaVIM-like, and blaADC-like genes was performed for isolates that showed, at least, two positive results of three for both AmpC and carbapenemases phenotypic screening tests (obvious activity), in addition to GP3 (for comparison). Detection of blaoxa-51like and blaADC-like genes preceded by ISAba1 was also performed. Results: Antibiogram of 69 pure Acinetobacter baumannii isolates resulted in 57, 64, and 2 isolates enrolled into GP1, GP2, and GP3, respectively. Carbapenemase activity was shown by 49(85.9%) isolate using MHT. Metallo-β-lactamases screening revealed 32(65.3%) and 35(71.4%) using DDST and CDT, respectively.AmpC activity was shown by 43(67.2%) and 50 (78.1%) isolates using AmpC disk test with Tris-EDTA, and both DDST and CDT, respectively. Twenty-seven isolates showed obvious activity, all of them (100%) were harboring blaoxa-51like and blaADC-like genes, while blaoxa-23like, blaIMP-like andblaVIM-like genes were harbored by 23(85.2%), 9 (33.%) and no isolate respectively. Only 12 (44.4%) isolates harbored blaoxa-51like and blaADC-like genes preceded by ISAba1. GP3 isolates showed only positive blaoxa-51like and blaADC-like genes. Conclusion: It is not possible to correlate resistance with presence of blaoxa-51like and blaADC-like genes and presence of ISAba1 was immediate as transcriptional promoter. A blaoxa-23like gene played an important role in carbapenem resistance when compared with blaIMP-like and blaVIM-like gene.

Keywords: acinetobacter, beta-lactams, resistance, antimicrobial agents

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Authors: Y. Hajjam, I. T. Alami, S. M. Udupa, S. Cherkaoui

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Faba bean (Vicia faba L.) is an important food legume crop in Morocco. It is mainly used as human food and feed for animals. Faba bean also plays an important role in cereal-based cropping systems, when rotated with cereals it improves soil fertility by fixing N2 in root nodules mediated by Rhizobium. Both faba bean and its biological nitrogen fixation symbiotic bacterium Rhizobium are affected by different stresses such as: salinity, drought, pH, heavy metal, and the uptake of inorganic phosphate compounds. Therefore, the aim of the present study was to evaluate the phenotypic diversity among the faba bean rhizobial isolates and to select the tolerant strains that can fix N2 under environmental constraints for inoculation particularly for affected soils, in order to enhance the productivity of faba bean and to improve soil fertility. Result have shown that 62% of isolates were fast growing with the ability of producing acids compounds , while 38% of isolates are slow growing with production of alkalins. Moreover, 42.5% of these isolates were able to solubilize inorganic phosphate Ca3(PO4)2 and the index of solubilization was ranged from 2.1 to 3.0. The resistance to extreme pH, temperature, water stress heavy metals and antibiotics lead us to classify rhizobial isolates into different clusters. Finally, the authentication test under greenhouse conditions showed that 55% of the rhizobial isolates could induce nodule formation on faba bean (Vicia faba L.) under greenhouse experiment. This phenotypic characterization may contribute to improve legumes and non legumes crops especially in affected soils and also to increase agronomic yield in the dry areas.

Keywords: rhizobia, vicia faba, phenotypic characterization, nodule formation, environmental constraints

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Authors: Zeynep Yazgan, Gökhan Aygün, Reyhan Çalışkan

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Objective: Invasive fungal infections are a serious threat in terms of morbidity and mortality, especially in immunocompromised patients. The most frequently isolated agents are Aspergillus genus fungi, and sensitivity to azoles, which are the first choice in treatment, decreases. In our study, we aimed to investigate the use of the agar plate screening method as a fast, easy, and practical method in determining azole resistance in Aspergillus spp. species. Methods: Our study was conducted with 125 Aspergillus spp. isolates produced from various clinical samples. Aspergillus spp. isolates were identified by conventional methods and azole resistance was determined by gradient test and agar plate screening method. Broth microdilution method was applied to resistant isolates, and CypA-L98H and CypA-M220 mutations in the cyp51A gene were investigated. Results: In our study, 55 A. fumigatus complex (44%), 42 A. flavus (33.6%), 6 A. terreus (5%), 4 A. niger (3%) and 18 Aspergillus spp. (14%) were identified. With the gradient test method, resistance to VOR and POS was detected in 1 (1.8%) of A.fumigatus isolates, and resistance to ITR was detected in 3 (5.45%). With the agar plate method, 1 of the A.fumigatus isolates (1.8%) had VOR, ITR, POS, 1 of the A.terreus isolates (16.7%) had VOR, 1 of the A.niger isolates (25%) had ITR. Resistance to VOR and POS was detected in 2 Aspergillus spp. isolates (11%), and resistance to ITR was detected in 1 (5.6%). Sensitivity and specificity were determined as 100% for VOR and POS in A. fumigatus species, 33.3% and 100% for ITR, respectively, 100% for ITR in A. flavus species, and 100% for ITR and POS in A. terreus species. By broth microdilution method in 7 isolates in which resistance was detected by gradient test and/or agar plate screening method; 1 A.fumigatus resistant to ITR, VOR, POS, 2 A.fumigatus resistant to ITR, 2 Aspergillus spp. ITR, VOR, POS MICs were determined as 2µg/ml and 8µg/ml, 8µg/ml and >32µg/ml, 0.5µg/ml and 4µg/ml, respectively. CypA-L98H mutations were detected in 5 of these isolates, CypA-M220 mutations were detected in 6, and no mutation was detected in 1. CypA-L98H and CypA-M220 mutations were detected in 1 isolate for which resistance was not detected. Conclusion: The need for rapid antifungal susceptibility screening tests is increasing in the treatment of aspergillosis. Although the sensitivity of the agar plate method was determined to be 33.3% for A.fumigatus ITR in our study, its sensitivity and specificity were determined to be 100% for ITR, VOR, and POS in other species. The low sensitivity value detected for A.fumigatus showed that agar plate drug concentrations should be updated in accordance with the latest regulations of EUCAST guidelines. The CypA-L98H and CypA-M220 mutations detected in our study suggested that the distribution of azole resistance-related mutations in different regions in our country should be investigated. In conclusion, it is thought that the agar plate method, which can be easily applied to detect azole resistance, is a fast and practical method in routine use and can contribute to both the determination of effective treatment strategies and the generation of epidemiological data.

Keywords: Aspergillus, agar plate, azole resistance, cyp51A, cypA-L98H, cypA-M220

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