Abstract: Sediment and mangrove root samples from Iko River
Estuary, Nigeria were analyzed for microbial and polycyclic
aromatic hydrocarbon (PAH) content. The total heterotrophic
bacterial (THB) count ranged from 1.1x107 to 5.1 x107 cfu/g, total
fungal (TF) count ranged from 1.0x106 to 2.7x106 cfu/g, total
coliform (TC) count ranged from 2.0x104 to 8.0x104cfu/g while
hydrocarbon utilizing bacterial (HUB) count ranged from 1.0x 105 to
5.0 x 105cfu/g. There was a range of positive correlation (r = 0.72 to
0.93) between THB count and total HUB count, respectively. The
organisms were Staphylococcus aureus, Bacillus cereus,
Flavobacterium breve, Pseudomonas aeruginosa, Erwinia
amylovora, Escherichia coli, Enterobacter sp, Desulfovibrio sp,
Acinetobacter iwoffii, Chromobacterium violaceum, Micrococcus
sedentarius, Corynebacterium sp, and Pseudomonas putrefaciens.
The PAH were Naphthalene, 2-Methylnaphthalene, Acenapthylene,
Acenaphthene, Fluorene, Phenanthene, Anthracene, Fluoranthene,
Pyrene, Benzo(a)anthracene, Chrysene, Benzo(b)fluoranthene,
Benzo(k)fluoranthene, Benzo(a)pyrene, Dibenzo(a,h)anthracene,
Benzo(g,h,l)perylene ,Indeno(1,2,3-d)pyrene with individual PAH
concentrations that ranged from 0.20mg/kg to 1.02mg/kg, 0.20mg/kg
to 1.07mg/kg and 0.2mg/kg to 4.43mg/kg in the benthic sediment,
epipellic sediment and mangrove roots, respectively. Total PAH
ranged from 6.30 to 9.93mg/kg, 6.30 to 9.13mg/kg and 9.66 to
16.68mg/kg in the benthic sediment, epipellic sediment and
mangrove roots, respectively. The high concentrations in the
mangrove roots are indicative of bioaccumulation of the pollutant in
the plant tissue. The microorganisms are of ecological significance
and the detectable quantities of polycyclic aromatic hydrocarbon
could be partitioned and accumulated in tissues of infaunal and
epifaunal organisms in the study area.
Abstract: The purpose of this study was to elucidate the factors affecting antimicrobial effectiveness of essential oils against food spoilage and pathogenic bacteria. The minimum inhibition concentrations (MIC) of the essential oils, were determined by turbidimetric technique using Biocreen C, analyzer. The effects of pH ranging from 7.3 to 5.5 in absence and presence of essential oils and/or NaCl on the lag time and mean generation time of the bacteria at 370C, were carried out and results were determined showed that, combination of low pH and essential oil at 370C had additive effects against the test micro-organisms. The combination of 1.2 % (w/v) of NaCl and clove essential oil at 0.0325% (v/v) was effective against E. coli. The use of concentrations less than MIC in combination with low pH and or NaCl has the potential of being used as an alternative to “traditional food preservatives".
Abstract: Environmental micro-organisms include a large number of taxa and some species that are generally considered nonpathogenic, but can represent a risk in certain conditions, especially for elderly people and immunocompromised individuals. Chemotaxonomic identification techniques are powerful tools for environmental micro-organisms, and cellular fatty acid methyl esters (FAME) content is a powerful fingerprinting identification technique. A system based on an unsupervised artificial neural network (ANN) was set up using the fatty acid profiles of standard bacterial strains, obtained by gas-chromatography, used as learning data. We analysed 45 certified strains belonging to Acinetobacter, Aeromonas, Alcaligenes, Aquaspirillum, Arthrobacter, Bacillus, Brevundimonas, Enterobacter, Flavobacterium, Micrococcus, Pseudomonas, Serratia, Shewanella and Vibrio genera. A set of 79 bacteria isolated from a drinking water line (AMGA, the major water supply system in Genoa) were used as an example for identification compared to standard MIDI method. The resulting ANN output map was found to be a very powerful tool to identify these fresh isolates.
Abstract: Proteomics is one of the largest areas of research for
bioinformatics and medical science. An ambitious goal of proteomics
is to elucidate the structure, interactions and functions of all proteins
within cells and organisms. Predicting Protein-Protein Interaction
(PPI) is one of the crucial and decisive problems in current research.
Genomic data offer a great opportunity and at the same time a lot of
challenges for the identification of these interactions. Many methods
have already been proposed in this regard. In case of in-silico
identification, most of the methods require both positive and negative
examples of protein interaction and the perfection of these examples
are very much crucial for the final prediction accuracy. Positive
examples are relatively easy to obtain from well known databases. But
the generation of negative examples is not a trivial task. Current PPI
identification methods generate negative examples based on some
assumptions, which are likely to affect their prediction accuracy.
Hence, if more reliable negative examples are used, the PPI prediction
methods may achieve even more accuracy. Focusing on this issue, a
graph based negative example generation method is proposed, which
is simple and more accurate than the existing approaches. An
interaction graph of the protein sequences is created. The basic
assumption is that the longer the shortest path between two
protein-sequences in the interaction graph, the less is the possibility of
their interaction. A well established PPI detection algorithm is
employed with our negative examples and in most cases it increases
the accuracy more than 10% in comparison with the negative pair
selection method in that paper.
Abstract: The comparative analysis of different taxonomic
groups of microorganisms isolated from dark chernozem soils under
different agricultures (alfalfa, melilot, sainfoin, soybean, rapeseed) at
Almaty region of Kazakhstan was conducted. It was shown that the
greatest number of micromycetes was typical to the soil planted with
alfalfa and canola. Species diversity of micromycetes markedly
decreases as it approaches the surface of the root, so that the species
composition in the rhizosphere is much more uniform than in the
virgin soil. Promising strains of microscopic fungi and yeast with
plant growth-promoting activity to agricultures were selected. Among
the selected fungi there are representatives of Penicillium bilaiae,
Trichoderma koningii, Fusarium equiseti, Aspergillus ustus. The
highest rates of growth and development of seedlings of plants
observed under the influence of yeasts Aureobasidium pullulans,
Rhodotorula mucilaginosa, Metschnikovia pulcherrima. Using
molecular - genetic techniques confirmation of the identification
results of selected micromycetes was conducted.
Abstract: Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Abstract: The development of the poultry industry in Albania is mainly based on the existence of intensive modern farms with huge capacities, which often are mixed with other forms. Colibacillosis is commonly displayed regardless of the type of breeding, delivering high mortality in poultry industry. The mechanisms with which pathogen enterobacters are able to cause the infection in poultry are not yet clear. The routine diagnose in the field, followed by isolation of E. coli and species of Salmonella genres in reference laboratories cannot lead in classification or full recognition of circulative strains in a territory, if it is not performed a differentiation among the present microorganisms in intensive farms and those in rural areas. In this study were isolated 1.496 strains of E. coli and 378 Salmonella spp. This study, presents distribution of poultry pathogenosity of E.coli and Salmonella spp., based on the usage of innovative diagnostic methods.
Abstract: The agriculture lignocellulosic by-products are receiving increased attention, namely in the search for filter materials that retain contaminants from water. These by-products, specifically almond and hazelnut shells are abundant in Portugal once almond and hazelnuts production is a local important activity. Hazelnut and almond shells have as main constituents lignin, cellulose and hemicelluloses, water soluble extractives and tannins. Along the adsorption of heavy metals from contaminated waters, water soluble compounds can leach from shells and have a negative impact in the environment. Usually, the chemical characterization of treated water by itself may not show environmental impact caused by the discharges when parameters obey to legal quality standards for water. Only biological systems can detect the toxic effects of the water constituents. Therefore, the evaluation of toxicity by biological tests is very important when deciding the suitability for safe water discharge or for irrigation applications.
The main purpose of the present work was to assess the potential impacts of waters after been treated for heavy metal removal by hazelnut and almond shells adsorption systems, with short term acute toxicity tests.
To conduct the study, water at pH 6 with 25 mg.L-1 of lead, was treated with 10 g of shell per litre of wastewater, for 24 hours. This procedure was followed for each bark. Afterwards the water was collected for toxicological assays; namely bacterial resistance, seed germination, Lemna minor L. test and plant grow. The effect in isolated bacteria strains was determined by disc diffusion method and the germination index of seed was evaluated using lettuce, with temperature and humidity germination control for 7 days. For aquatic higher organism, Lemnas were used with 4 days contact time with shell solutions, in controlled light and temperature. For terrestrial higher plants, biomass production was evaluated after 14 days of tomato germination had occurred in soil, with controlled humidity, light and temperature.
Toxicity tests of water treated with shells revealed in some extent effects in the tested organisms, with the test assays showing a close behaviour as the control, leading to the conclusion that its further utilization may not be considered to create a serious risk to the environment.
Abstract: In the present study, the effect of ferrous sulfate concentration and total solids on bioleaching of heavy metals from sewage sludge has been examined using indigenous iron-oxidizing microorganisms. The experiments on effects of ferrous sulfate concentrations on bioleaching were carried out using ferrous sulfate of different concentrations (5-20 g L-1) to optimize the concentration of ferrous sulfate for maximum bioleaching. A rapid change in the pH and ORP took place in first 2 days followed by a slow change till 16th day in all the sludge samples. A 10 g L-1 ferrous sulfate concentration was found to be sufficient in metal bioleaching in the following order: Zn: 69%>Cu: 52%>Cr: 46%>Ni: 45. Further, bioleaching using 10 g/L ferrous sulfate was found to be efficient up to 20 g L-1 sludge solids concentration. The results of the present study strongly indicate that using 10 g L-1 ferrous sulfate indigenous iron-oxidizing microorganisms can bring down pH to a value needed for significant metal solubilization.
Abstract: The overall objective of this research is a strain
improvement technology for efficient pectinase production. A novel
cells cultivation technology by immobilization of fungal cells has
been studied in long time continuous fermentations. Immobilization
was achieved by using of new material for absorption of stores of
immobilized cultures which was for the first time used for
immobilization of microorganisms. Effects of various conditions of
nitrogen and carbon nutrition on the biosynthesis of pectolytic
enzymes in Aspergillus awamori 1-8 strain were studied. Proposed
cultivation technology along with optimization of media components
for pectinase overproduction led to increased pectinase productivity
in Aspergillus awamori 1-8 from 7 to 8 times. Proposed technology
can be applied successfully for production of major industrial
enzymes such as α-amylase, protease, collagenase etc.
Abstract: fibers of pure cellulose can be made from some bacteria such as acetobacter xylinum. Bacterial cellulose fibers are very pure, tens of nm across and about 0.5 micron long. The fibers are very stiff and, although nobody seems to have measured the strength of individual fibers. Their stiffness up to 70 GPa. Fundamental strengths should be at least greater than those of the best commercial polymers, but best bulk strength seems to about the same as that of steel. They can potentially be produced in industrial quantities at greatly lowered cost and water content, and with triple the yield, by a new process. This article presents a critical review of the available information on the bacterial cellulose as a biological nonwoven fabric with special emphasis on its fermentative production and applications. Characteristics of bacterial cellulose biofabric with respect to its structure and physicochemical properties are discussed. Current and potential applications of bacterial cellulose in textile, nonwoven cloth, paper, films synthetic fiber coating, food, pharmaceutical and other industries are also presented.
Abstract: The antimicrobial, antiplasmid and cytotoxic activities of marine algae Halimeda opuntia and Sarconema filiforme were investigated. Antimicrobial bioassay against some human pathogenic bacteria and yeast were conducted using disc diffusion method. Halimeda extract exhibited antibacterial activity against six species of microrganisms, with significant inhibition against Staphylococcus aureus. While Sarconema extract was better potent as antifungal against Candida albicans. Comparative antibacterial studies showed that Halimeda extract showed equivalent or better activity as compared with commercial antibiotic when tested against Staphylococcus aureus. Further tests conducted using dilution method showed both extracts as having bacteriostatic mode of action against the tested microorganisms. Methanol extract of two species showed significant cytotoxicity (LC50
Abstract: 17α-ethinylestradiol (EE2) is a recalcitrant micropollutant which is found in small amounts in municipal wastewater. But these small amounts still adversely affect for the reproductive function of aquatic organisms. Evidence in the past suggested that full-scale WWTPs equipped with nitrification process enhanced the removal of EE2 in the municipal wastewater. EE2 has been proven to be able to be transformed by ammonia oxidizing bacteria (AOB) via co-metabolism. This research aims to clarify the EE2 degradation pattern by different consortium of ammonia oxidizing microorganism (AOM) including AOA (ammonia oxidizing archaea) and investigate contribution between the existing ammonia monooxygenase (AMO) and new synthesized AOM. The result showed that AOA or AOB of N. oligotropha cluster in enriched nitrifying activated sludge (NAS) from 2mM and 5mM, commonly found in municipal WWTPs, could degrade EE2 in wastewater via co-metabolism. Moreover, the investigation of the contribution between the existing ammonia monooxygenase (AMO) and new synthesized AOM demonstrated that the new synthesized AMO enzyme may perform ammonia oxidation rather than the existing AMO enzyme or the existing AMO enzyme may has a small amount to oxidize ammonia.
Abstract: The objectives were to identify cyanide-degrading
bacteria and study cyanide removal efficiency. Agrobacterium
tumefaciens SUTS 1 was isolated. This is a new strain of
microorganisms for cyanide degradation. The maximum growth rate
of SUTS 1 obtained 4.7 × 108 CFU/ml within 4 days. The cyanide
removal efficiency was studied at 25, 50, and 150 mg/L cyanide. The
residual cyanide, ammonia, nitrate, nitrite, pH, and cell counts were
analyzed. At 25 and 50 mg/L cyanide, SUTS 1 obtained similar
removal efficiency approximately 87.50%. At 150 mg/L cyanide,
SUTS 1 enhanced the cyanide removal efficiency up to 97.90%. Cell
counts of SUTS 1 increased when the cyanide concentration was set
at lower. The ammonia increased when the removal efficiency
increased. The nitrate increased when the ammonia decreased but the
nitrite did not detect in all experiments. pH values also increased
when the cyanide concentrations were set at higher.
Abstract: Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.
Abstract: Austenite and Martensite indicate the phases of solids undergoing phase transformation which we usually associate with materials and not with living organisms. This article provides an overview of bacterial proteins and structures that are undergoing phase transformation and suggests its probable effect on mechanical behavior. The context is mainly within the role of phase transformations occurring in the flagellum of bacteria. The current knowledge of molecular mechanism leading to phase variation in living organisms is reviewed. Since in bacteria, each flagellum is driven by a separate motor, similarity to a Differential drive in case of four-wheeled vehicles is suggested. It also suggests the application of the mechanism in which bacteria changes its direction of movement to facilitate single point turning of a multi-wheeled vehicle. Finally, examples are presented to illustrate that the motion due to phase transformation of flagella in bacteria can start a whole new research on motion mechanisms.
Abstract: Dextran is a D-glucose polymer which is produced by
Leuconostoc mesenteroides grown in a sucrose-rich media. The
organism was obtained from the Persian Type Culture Collection
(PTCC) and was transferred in MRS broth medium at 30°C and pH
6.8 for 24 h. After preparation of inoculums, organisms were
inoculated into five liquid fermentation media containing either
molasses or cheese whey or different combinations of cheese whey
and molasses. After certain fermentation period, the produced
dextran was separated and dried. Dextran yield was calculated and
significant differences in different media were observed.
Furthermore, FT-IR analysis was performed and the results showed
that there were no significant differences in the produced dextran
structures.
Abstract: To decompose organochlorides by bioremediation, co-culture biohydrogen producer and dehalogenation microorganisms is a useful method. In this study, we combined these two characteristics from a biohydrogen producer, Rhodopseudomonas palustris, and a dehalogenation microorganism, Pseudomonas putida, to enchance halorespiration in R. palustris. The genes encoding cytochrome P450cam system (camC, camA, and camB) from P. putida were expressed in R. palustris with designated expression plasmid. All tested strains were cultured to log phase then presented pentachloroethane (PCA) in media. The vector control strain could degrade PCA about 78% after 16 hours, however, the cytochrome P450cam system expressed strain, CGA-camCAB, could completely degrade PCA in 12 hours. While taking chlorinated aromatic, 3-chlorobenzoate, as sole carbon source or present benzoate as co-substrate, CGA-camCAB presented faster growth rate than vector control strain.
Abstract: An implant elicits a biological response in the
surrounding tissue which determines the acceptance and long-term
function of the implant. Dental implants have become one of the
main therapy methods in clinic after teeth lose. A successful implant
is in contact with bone and soft tissue represent by fibroblasts. In our
study we focused on the interaction between six different chemically
and physically modified titanium implants (Tis-MALP, Tis-O, Tis-
OA, Tis-OPAAE, Tis-OZ, Tis-OPAE) with alveolar fibroblasts as
well as with five type of microorganisms (S. epidermis, S.mutans, S.
gordonii, S. intermedius, C.albicans). The analysis of microorganism
adhesion was determined by CFU (colony forming unite) and biofilm
formation. The presence of α3β1 and vinculin expression on alveolar
fibroblasts was demonstrated using phospho specific cell based
ELISA (PACE). Alveolar fibroblasts have the highest expression of
these proteins on Tis-OPAAE and Tis-OPAE. It corresponds with
results from bacterial adhesion and biofilm formation and it was
related to the lowest production of collagen I by alveolar fibroblasts
on Tis-OPAAE titanium disc.
Abstract: Gene, principal unit of inheritance, is an ordered
sequence of nucleotides. The genes of eukaryotic organisms include
alternating segments of exons and introns. The region of
Deoxyribonucleic acid (DNA) within a gene containing instructions
for coding a protein is called exon. On the other hand, non-coding
regions called introns are another part of DNA that regulates gene
expression by removing from the messenger Ribonucleic acid (RNA)
in a splicing process. This paper proposes to determine splice
junctions that are exon-intron boundaries by analyzing DNA
sequences. A splice junction can be either exon-intron (EI) or intron
exon (IE). Because of the popularity and compatibility of the
artificial neural network (ANN) in genetic fields; various ANN
models are applied in this research. Multi-layer Perceptron (MLP),
Radial Basis Function (RBF) and Generalized Regression Neural
Networks (GRNN) are used to analyze and detect the splice junctions
of gene sequences. 10-fold cross validation is used to demonstrate
the accuracy of networks. The real performances of these networks
are found by applying Receiver Operating Characteristic (ROC)
analysis.