Abstract: Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.
Abstract: Prickly pear (Opuntia spp) fruit has received renewed
interest since it contains a betalain pigment that has an attractive
purple colour for the production of juice. Prickly pear juice was
prepared by homogenizing the fruit and treating the pulp with 48 g of
pectinase from Aspergillus niger. Titratable acidity was determined
by diluting 10 ml prickly pear juice with 90 ml deionized water and
titrating to pH 8.2 with 0.1 N NaOH. Brix was measured using a
refractometer and ascorbic acid content assayed
spectrophotometrically. Colour variation was determined
colorimetrically (Hunter L.a.b.). Hunter L.a.b. analysis showed that
the red purple colour of prickly pear juice had been affected by juice
treatments. This was indicated by low light values of colour
difference meter (CDML*), hue, CDMa* and CDMb* values. It was
observed that non-treated prickly pear juice had a high (colour
difference meter of light) CDML* of 3.9 compared to juice
treatments (range 3.29 to 2.14). The CDML* significantly (p
Abstract: Interaction of inorganic water-soluble salts and building stones is studied in the paper. Two types of sandstone and one type of spongillite as representatives of materials used in historical masonry are subjected to experimental testing. Within the performed experiments, measurement of moisture and chloride concentration profiles is done in order to get input data for computational inverse analysis. Using the inverse analysis, moisture diffusivity and chloride diffusion coefficient of investigated materials are accessed. Additionally, the effect of salt presence on water vapor storage is investigated using dynamic vapor sorption device. The obtained data represents valuable information for restoration of historical masonry and give evidence on the performance of studied stones in contact with water soluble salts.
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: Kojic acid is an organic acid that is widely used as an ingredient for dermatological products, precursor for flavor enhancer and also as anti-inflammatory drug. The present study was undertaken to test the feasibility of pineapple residues as substrate for kojic acid production by Aspergillus flavus Link 44-1 via solid-state fermentation. The effect of initial moisture content, pH and incubation time on kojic acid fermentation was investigated. The best initial moisture content for kojic acid production from pineapple residues was observed at 70% (v/w) whereas initial culture pH 2.5 was identified to give high production of kojic acid. The optimal range of incubation time was identified between 8 and 14 days of incubation which corresponded to highest range of kojic acid produced. The results from this study pronounce the promising usability of pineapple residues as alternative substrate for kojic acid production by A. flavus Link 44-1.
Abstract: Plants are rich sources of bioactive compounds. In this study the photochemical screening of hexane, ethanolic and aqueous extracts of roots and latex of jojoba (Simmondsia chinensis) plant revealed the presence of saponins, tannins, alkaloids, steroids and glycosides. Ethanolic extract was found to be richer in these metabolites than hexane, aqueous extracts and latex. The extracts and latex displayed effective antimicrobial activity against Salmonella typhimurium, Bacillus cereus, Clostridium perfringens, Staphylococcus aureus, Escherichia coli, Candida albicans and Aspergillus flavus. The increase in volume of the extracts and latex caused more activity, as shown by zones of inhibition. Candida albicans growth was inhibited only by hexane extract. Jojoba latex was not effective against Candida albicans at 0.1 and 0.5 ml extracts concentration but showed 5mm zone of inhibition at (1.0 ml). Lower volume (0.1ml) of latex encouraged Aspergillus flavus growth, while at (1.00 ml) reduced its mycelial growth. Thus, jojoba root extracts and latex can be of potential natural antimicrobial agents.
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: Gluconic acid is one of interesting chemical products
in industries such as detergents, leather, photographic, textile, and
especially in food and pharmaceutical industries. Fermentation is an
advantageous process to produce gluconic acid. Mathematical
modeling is important in the design and operation of fermentation
process. In fact, kinetic data must be available for modeling. The
kinetic parameters of gluconic acid production by Aspergillus niger
in batch culture was studied in this research at initial substrate
concentration of 150, 200 and 250 g/l. The kinetic models used were
logistic equation for growth, Luedeking-Piret equation for gluconic
acid formation, and Luedeking-Piret-like equation for glucose
consumption. The Kinetic parameters in the model were obtained by
minimizing non linear least squares curve fitting.
Abstract: Thirty six samples from each (aerobic and anoxic)
activated sludge were collected from two wastewater treatment plants
with MBRs in Berlin, Germany. The samples were prepared for count
and definition of fungal isolates; these isolates were purified by
conventional techniques and identified by microscopic examination.
Sixty tow species belonging to 28 genera were isolated from
activated sludge samples under aerobic conditions (28 genera and 58
species) and anoxic conditions (26 genera and 52 species). The
obtained data show that, Aspergillus was found at 94.4% followed by
Penicillium 61.1 %, Fusarium (61.1 %), Trichoderma (44.4 %) and
Geotrichum candidum (41.6 %) species were the most prevalent in all
activated sludge samples. The study confirmed that fungi can thrive
in activated sludge and sporulation, but isolated in different numbers
depending on the effect of aeration system. Some fungal species in
our study are saprophytic, and other a pathogenic to plants and
animals.
Abstract: A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.
Abstract: Different agricultural waste peels were assessed for
their suitability to be used as primary substrates for the
bioremediation of free cyanide (CN-) by a cyanide-degrading fungus
Aspergillus awamori isolated from cyanide containing wastewater.
The bioremediated CN- concentration were in the range of 36 to 110
mg CN-/L, with Orange (C. sinensis) > Carrot (D. carota) > Onion
(A. cepa) > Apple (M. pumila), being chosen as suitable substrates
for large scale CN- degradation processes due to: 1) the high
concentration of bioremediated CN-, 2) total reduced sugars released
into solution to sustain the biocatalyst, and 3) minimal residual NH4-
N concentration after fermentation. The bioremediation rate constants
(k) were 0.017h-1 (0h < t < 24h), with improved bioremediation rates
(0.02189h-1) observed after 24h. The averaged nitrilase activity was
~10 U/L.
Abstract: Prickly pear juice has received renewed attention with regard to the effects of processing and preservation on its sensory qualities (colour, taste, flavour, aroma, astringency, visual browning and overall acceptability). Juice was prepared by homogenizing fruit and treating the pulp with pectinase (Aspergillus niger). Juice treatments applied were sugar addition, acidification, heat-treatment, refrigeration, and freezing and thawing. Prickly pear pulp and juice had unique properties (low pH 3.88, soluble solids 3.68 oBrix and high titratable acidity 0.47). Sensory profiling and descriptive analyses revealed that non-treated juice had a bitter taste with high astringency whereas treated prickly pear was significantly sweeter. All treated juices had a good sensory acceptance with values approximating or exceeding 7. Regression analysis of the consumer sensory attributes for non-treated prickly pear juice indicated an overwhelming rejection, while treated prickly pear juice received overall acceptability. Thus, educed favourable sensory responses and may have positive implications for consumer acceptability.
Abstract: Empty Fruit Bunches (EFB) and Palm Oil Mill
Effluent (POME) are two main wastes from oil palm industries which
contain rich lignocellulose. Degradation of EFB and POME by
microorganisms will produce hydrolytic enzyme which will degrade
cellulose and hemicellulose during composting process. However,
normal composting takes about four to six months to reach maturity.
Hence, application of fungi into compost can shorten the period of
composting. This study identifies the effect of xylanase and cellulase
produced by Aspergillus niger and Trichoderma virens on
composting process using EFB and POME. The degradation of EFB
and POME indicates the lignocellulolytic capacity of Aspergillus
niger and Trichoderma virens with more than 7% decrease in
hemicellulose and more than 25% decrease in cellulose for both
inoculated compost. Inoculation of Aspergillus niger and
Trichoderma virens also increased the enzyme activities during the
composting period compared to the control compost by 21% for both
xylanase and cellulase. Rapid rise in the activities of cellulase and
xylanase was observed by Aspergillus niger with the highest
activities of 14.41 FPU/mg and 3.89 IU/mg, respectively. Increased
activities of cellulase and xylanase also occurred in inoculation of
Trichoderma virens with the highest activities obtained at 13.21
FPU/mg and 4.43 IU/mg, respectively. Therefore, it is evident that
the inoculation of fungi can increase the enzyme activities hence
effectively degrading the EFB and POME.
Abstract: An original Direct Numerical Simulation (DNS) method to tackle the problem of particulate flows at moderate to high concentration and finite Reynolds number is presented. Our method is built on the framework established by Glowinski and his coworkers [1] in the sense that we use their Distributed Lagrange Multiplier/Fictitious Domain (DLM/FD) formulation and their operator-splitting idea but differs in the treatment of particle collisions. The novelty of our contribution relies on replacing the simple artificial repulsive force based collision model usually employed in the literature by an efficient Discrete Element Method (DEM) granular solver. The use of our DEM solver enables us to consider particles of arbitrary shape (at least convex) and to account for actual contacts, in the sense that particles actually touch each other, in contrast with the simple repulsive force based collision model. We recently upgraded our serial code, GRIFF 1 [2], to full MPI capabilities. Our new code, PeliGRIFF 2, is developed under the framework of the full MPI open source platform PELICANS [3]. The new MPI capabilities of PeliGRIFF open new perspectives in the study of particulate flows and significantly increase the number of particles that can be considered in a full DNS approach: O(100000) in 2D and O(10000) in 3D. Results on the 2D/3D sedimentation/fluidization of isometric polygonal/polyedral particles with collisions are presented.
Abstract: The parametrical study of Shrouded Contra-rotating
Rotor was done in this paper based on 2D axisymmetric simulations.
The calculations were made with an actuator disk as double rotor
model. It objects to explore and quantify the effects of different shroud
geometry parameters mainly using the performance of power loading
(PL), which could evaluate the whole propulsion system capability as
5 Newtontotal thrust generationfor hover demand. The numerical
results show that:The increase of nozzle radius is desired but limited
by the flow separation, its optimal design is around 1.15 times rotor
radius, the viscosity effects greatly constraint the influence of nozzle
shape, the divergent angle around 10.5° performs best for chosen
nozzle length;The parameters of inlet such as leading edge curvature,
radius and internal shape do not affect thrust great but play an
important role in pressure distribution which could produce most part
of shroud thrust, they should be chosen according to the reduction of
adverse pressure gradients to reduce the risk of boundary separation.
Abstract: This study was conducted to evaluate the antifungal
activities of Cinnamomum zeylanicum and Origanum vulgare L.
essential oil against Aspergillus flavus in culture media and tomato
paste. 200 ppm of cinnamon and 500 ppm of oregano completely
inhibited A. flavus growth in culture media, while in tomato paste 300
ppm of cinnamon and 200 ppm of oregano had the same effect. Test
panel evaluations revealed that samples with 100 and 200 ppm
cinnamon were acceptable. The results may suggest the potential use
of Cinnamomum zeylanicum essential oil as natural preservative in
tomato paste.
Abstract: The complex structure of lignocellulose leads to great
difficulties in converting it to fermentable sugars for the ethanol
production. The major hydrolysis impediments are the crystallinity of
cellulose and the lignin content. To improve the efficiency of
enzymatic hydrolysis, microbial pretreatment of corncob was
investigated using two bacterial strains of Bacillus subtilis A 002 and
Cellulomonas sp. TISTR 784 (expected to break open the crystalline
part of cellulose) and lignin-degrading fungus, Phanerochaete
sordida SK7 (expected to remove lignin from lignocellulose). The
microbial pretreatment was carried out with each strain under its
optimum conditions. The pretreated corncob samples were further
hydrolyzed to produce reducing glucose with low amounts of
commercial cellulase (25 U·g-1 corncob) from Aspergillus niger. The
corncob samples were determined for composition change by X-ray
diffraction (XRD), Fourier transform infrared spectroscopy (FTIR),
and scanning electron microscope (SEM). According to the results,
the microbial pretreatment with fungus, P. sordida SK7 was the most
effective for enhancing enzymatic hydrolysis, approximately, 40%
improvement.
Abstract: The bioassay-guided isolation and purification of an
ethyl acetate extract of Aspergillus terreus MC751 led to the
characterization of butyrolactone I as an antidiabetic and antioxidant.
The antidiabetic activity of butyrolactone I was evaluated by α-
glucosidase and α-amylase inhibition assays. Butyrolactone I
demonstrated significant concentration-dependent, mixed-type
inhibitory activity against yeast α-glucosidase with an IC50 of 54μM.
However, the compound exhibited less activity against rat intestinal
α-glucosidase and α-amylase. This is the first report on α-glucosidase
inhibitory activity of butyrolactone I. The antioxidative activity of
butyrolactone I was evaluated based on scavenging effects on 1,1-
diphenyl-2-picrylhydrazyl (DPPH) (IC50 =51 μM) and hydrogen
peroxide (IC50= 141 μM) radicals as well as a reducing power assay.
The results suggest that butyrolactone I is a promising antidiabetic as
well as antioxidant and should be considered for clinical trials.
Abstract: The segmentation of endovascular tools in fluoroscopy images can be accurately performed automatically or by minimum user intervention, using known modern techniques. It has been proven in literature, but no clinical implementation exists so far because the computational time requirements of such technology have not yet been met. A classical segmentation scheme is composed of edge enhancement filtering, line detection, and segmentation. A new method is presented that consists of a vector that propagates in the image to track an edge as it advances. The filtering is performed progressively in the projected path of the vector, whose orientation allows for oriented edge detection, and a minimal image area is globally filtered. Such an algorithm is rapidly computed and can be implemented in real-time applications. It was tested on medical fluoroscopy images from an endovascular cerebral intervention. Ex- periments showed that the 2D tracking was limited to guidewires without intersection crosspoints, while the 3D implementation was able to cope with such planar difficulties.
Abstract: Isobaric vapor-liquid equilibrium measurements are reported for the binary mixtures of Mesitylene + 1-Heptanol and Mesitylene + 1-Octanol at 97.3 kPa. The measurements have been performed using a vapor recirculating type (modified Othmer's) equilibrium still. Both the mixtures show positive deviation from ideality. The Mesitylene + 1-Heptanol mixture forms an azeotrope whereas Mesitylene + 1- Octanol form a non – azeotropic mixture. The activity coefficients have been calculated taking into consideration the vapor phase nonideality. The data satisfy the thermodynamic consistency tests of Herington, and Hirata. The activity coefficients have been satisfactorily correlated by means of the Margules, Redlich-Kister, Wilson, Black, and NRTL equations. The activity coefficient values have also been obtained by UNIFAC method.