Abstract: A New features are extracted and compared to
improve the prediction of protein-protein interactions. The basic idea
is to select and use the best set of features from the Tensor matrices
that are produced by the frequency vectors of the protein sequences.
Three set of features are compared, the first set is based on the
indices that are the most common in the interacting proteins, the
second set is based on the indices that tend to be common in the
interacting and non-interacting proteins, and the third set is
constructed by using random indices. Moreover, three encoding
strategies are compared; that are based on the amino asides polarity,
structure, and chemical properties. The experimental results indicate
that the highest accuracy can be obtained by using random indices
with chemical properties encoding strategy and support vector
machine.
Abstract: Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.
Abstract: According to FDA (Food and Drug Administration of the United States), vinegar is definedas a sour liquid containing at least 4 grams acetic acid in 100 cubic centimeter (4% solution of acetic acid) of solution that is produced from sugary materials by alcoholic fermentation. In the base of microbial starters, vinegars could be contained of more than 50 types of volatile and aromatic substances that responsible for their sweet taste and smelling. Recently the vinegar industry has a great proportion in agriculture, food and microbial biotechnology. The acetic acid bacteria are from the family Acetobacteraceae. Regarding to the latest version of Bergy-s Mannual of Systematic Bacteriology that has categorized bacteria in the base of their 16s RNA differences, the most important acetic acid genera are included Acetobacter (genus I), Gluconacetobacter (genus VIII) and Gluconobacter (genus IX). The genus Acetobacter that is primarily used in vinegar manufacturing plants is a gram negative, obligate aerobe coccus or rod shaped bacterium with the size 0.6 - 0.8 X 1.0 - 4.0 μm, nonmotile or motile with peritrichous flagella and catalase positive – oxidase negative biochemically. Some strains are overoxidizer that could convert acetic acid to carbon dioxide and water.In this research one Acetobacter native strain with high acetic acid productivity was isolated from Iranian white – red cherry. We used two specific culture media include Carr medium [yeast extract, 3%; ethanol, 2% (v/v); bromocresol green, 0.002%; agar, 2% and distilled water, 1000 ml], Frateur medium [yeast extract, 10 g/l; CaCO3, 20 g/l; ethanol, 20 g/l; agar, 20 g/l and distilled water, 1000 ml] and an industrial culture medium. In addition to high acetic acid production and high growth rate, this strain had a good tolerance against ethanol concentration that was examined using modified Carr media with 5%, 7% and 9% ethanol concentrations. While the industrial strains of acetic acid bacteria grow in the thermal range of 28 – 30 °C, this strain was adapted for growth in 34 – 36 °C after 96 hours incubation period. These dramatic characteristics suggest a potential biotechnological strain in production of cherry vinegar with a sweet smell and different nutritional properties in comparison to recent vinegar types. The lack of growth after 24, 48 and 72 hours incubation at 34 – 36 °C and the growth after 96 hours indicates a good and fast thermal flexibility of this strain as a significant characteristic of biotechnological and industrial strains.
Abstract: An experimental study of anaerobic treatment was performed by hybrid upflow anaerobic sludge blanket (HUASB) reactor to treat produced water (PW) of an onshore crude oil terminal (COD: 1597 mg/L, NH3-N: 14.7 mg/L, phenol: 13.8 mg/L, BOD5: 862 mg/L, sodium: 6240 mg/L and chloride 9530 mg/L). The produced water with high salinity and other toxic substances will inhibit the methanogens performance if there is no adaptation on biomass before anaerobic digestion. COD removal from produced water was investigated at five different dilutions of produced water and tap water (TW) without any nutrient addition and pre-treatment. The dilution ratios were 1PW:4TW, 2PW:3TW, 3PW:2TW, 4PW:1TW and 5PW:0TW. The reactor was evaluated at mesophilic operating condition (35 ± 2 °C) at 5 days of HRT for 250 days continuous feed. The average COD removals for 1PW:4TW, 2PW:3TW, 3PW:2TW, 4PW:1TW and 5PW:0TW were found to be approximately 76.1%, 73.8%, 70.3%, 46.3% and 61.82% respectively, with final average effluent COD of 123.7 mg/L, 240 mg/L, 294 mg/L, 589 mg/L and 738 mg/L, respectively.
Abstract: To unveil the mechanism of fast autooxidation of fish
myoglobins, the effect of temperature on the structural change of tuna
myoglobin was investigated. Purified myoglobin was subjected to
preincubation at 5, 20, 50 and 40oC. Overall helical structural decay
through thermal treatment up to 95oC was monitored by circular
dichroism spectrometry, while the structural changes around the heme
pocket was measured by ultraviolet/visible absorption spectrophotometry.
As a result, no essential structural change of myoglobin
was observed under 30oC, roughly equivalent to their body
temperature, but the structure was clearly damaged at 40oC. The Soret
band absorption hardly differed irrespective of preincubation
temperature, suggesting that the structure around the heme pocket was
not perturbed even after thermal treatment.
Abstract: In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.
Abstract: Carbon nanotubes (CNTs) are attractive because of
their excellent chemical durability mechanical strength and electrical
properties. Therefore there is interest in CNTs for not only electrical
and mechanical application, but also biological and medical
application.
In this study, the dispersion power of surfactant-treated multiwalled
carbon nanotubes (MWCNTs) and their effect on the antibacterial
activity were examined. Surfactant was used sodium
dodecyl-benzenesulfonate (SDBS). UV-vis absorbance and
transmission electron microscopy(TEM) were used to characterize the
dispersion of MWCNTs in the aqueous phase, showing that the
surfactant molecules had been adsorbed onto the MWCNTs surface.
The surfactant-treated MWCNTs exhibited antimicrobial activities
to streptococcus mutans. The optical density growth curves and viable
cell number determined by the plating method suggested that the
antimicrobial activity of surfactant-treated MWCNTs was both
concentration and treatment time-dependent.
Abstract: Proteins levels produced by bacteria may be increased
in stressful surroundings, such as in the presence of antibiotics. It
appears that many antimicrobial agents or antibiotics, when used at
low concentrations, have in common the ability to activate or repress
gene transcription, which is distinct from their inhibitory effect.
There have been comparatively few studies on the potential of
antibiotics or natural compounds in nature as a specific chemical
signal that can trigger a variety of biological functions. Therefore,
this study was focusing on the effect of essential oils from
Cymbopogon flexuosus and C. nardus in regulating proteins
production by Bacillus subtilis ATCC 21332. The Minimum
Inhibition Concentrations (MICs) of both essential oils on B. subtilis
were determined by using microdilution assay, resulting 0.2% and
1.56% for each C. flexuosus and C. nardus subsequently. The
bacteria were further exposed to each essential oils at concentration
of 0.01XMIC for 2 days. The proteins were then isolated and
analyzed by sodium dodecyl sulfate polyacrylamide gel
electrophoresis (SDS-PAGE). Protein profile showed that a band
with approximate size of 250 kD was appeared for the treated
bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in
stressful condition with the presence of essential oils at low
concentration could induce the protein production.
Abstract: This paper reports optimization of characteristics of bioballistic transformation of spring soft wheat (Triticum aestivum L. cultivar Raduga) and getting of transgenic plants, carrying pea lectin gene. This gene will let to create new associative wheat symbiosis with nodule bacteria of field pea, which has growth encouraging, fungistatic and other useful characteristics.
Abstract: Lycopene, which can be extracted from plants and is
very popular for fruit intake, is restricted for healthy food development
due to its high price. On the other hand, it will get great safety
concerns, especially in the food or cosmetic application, if the raw
material of lycopene is produced by chemical synthesis. In this
project, we provide a key technology to bridge the limitation as
mentioned above. Based on the abundant bioresources of BCRC
(Bioresource Collection and Research Center, Taiwan), a promising
lycopene output will be anticipated by the introduction of fermentation
technology along with industry-related core energy. Our results
showed that addition of tween 80(0.2%) and span 20 produced higher
amount of lycopene. And piperidine, when was added at 48hr to the
cultivation medium, could promote lycopene excretion effectively
also.
Abstract: The aims of this paper are to study the efficacy of
chitosan nanoparticles in stimulating specific antibody against
A/H1N1 influenza antigen in mice. Chitosan nanoparticles (CSN)
were characterized by TEM. The results showed that the average size
of CSN was from 80nm to 106nm. The efficacy of A/H1N1 influenza
vaccine loaded on the surface of CSN showed that loading efficiency
of A/H1N1 influenza antigen on CSN was from 93.75 to 100%. Safe
property of the vaccine were tested. In 10 days post vaccination,
group of CSN 30 kDa and 300 kDa loaded A/H1N1 influenza antigen
were the rate of immune response on mice to be 100% (9/9) higher
than Al(OH)3 and other adjuvant. 100% mice in the experiment of all
groups had immune response in 20 days post vaccination. The results
also showed that HI titer of the group using CSN 300 kDa as an
adjuvant increased significantly up to 3971 HIU, over three-fold
higher than the Al(OH)3 adjuvant, chitosan (CS), and one hundredfold
than the A/H1N1 antigen only. Stability of the vaccine
formulation was investigated.
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 aim of the study was to investigate phytochemical
properties, antimicrobial activity and cytotoxicity of Aloe vera. The
phytochemical screening of the extracts of leaves of A. vera revealed
the presence of bioactive compounds such as alkaloids, tannins,
flavonoids phenolic compounds, and etc. with absence of cyanogenic
glycosides. Three different solvents such as methanol, ethanol and
Di-Methyl sulfoxide were used to screen the antimicrobial activity of
A. vera leaves against four human clinical pathogens by agar well
diffusion method. The maximum antibacterial activities were
observed in methanol extract followed by ethanol and Di-Methyl
sulfoxide. It was also found that remarkable antibacterial activities
with methanolic and ethanolic extracts of A. vera compared with the
standard antibiotic, tetracycline that was not active against E. coli
and S. boydii and supported the view that A. vera is a potent
antimicrobial agent compared with the conventional antibiotic.
Moreover, the brine shrimps (Artemia salina) toxicity test exhibited
LC50 value was 569.52 ppm. The resulting data indicated that the A.
vera plant have less toxic effects on brine shrimp. Hence, it is
signified that Aloe vera plant extract is safe to be used as an
antimicrobial agent.
Abstract: The full length mitochondrial small subunit ribosomal
(mt-rns) gene has been characterized for Ophiostoma novo-ulmi
subspecies americana. The gene was also characterized for
Ophiostoma ulmi and a group II intron was noted in the mt-rns gene
of O. ulmi. The insertion in the mt-rns gene is at position S952 and it
is a group IIB1 intron that encodes a double motif LAGLIDADG
homing endonuclease from an open reading frame located within a
loop of domain III. Secondary structure models for the mt-rns RNA
of O. novo-ulmi subsp. americana and O. ulmi were generated to
place the intron within the context of the ribosomal RNA. The in vivo
splicing of the O.ul-mS952 group II intron was confirmed with
reverse transcription-PCR. A survey of 182 strains of Dutch Elm
Diseases causing agents showed that the mS952 intron was absent in
what is considered to be the more aggressive species O. novo-ulmi
but present in strains of the less aggressive O. ulmi. This observation
suggests that the O.ul-mS952 intron can be used as a PCR-based
molecular marker to discriminate between O. ulmi and O. novo-ulmi
subsp. americana.
Abstract: Every 2-3 years the influenza B virus serves
epidemics. Neuraminidase (NA) is an important target for influenza
drug design. Although, oseltamivir, an oral neuraminidase drug, has
been shown good inhibitory efficiency against wild-type of influenza
B virus, the lower susceptibility to the R152K mutation has been
reported. Better understanding of oseltamivir efficiency and
resistance toward the influenza B NA wild-type and R152K mutant,
respectively, could be useful for rational drug design. Here, two
complex systems of wild-type and R152K NAs with oseltamivir
bound were studied using molecular dynamics (MD) simulations.
Based on 5-ns MD simulation, the loss of notable hydrogen bond and
decrease in per-residue decomposition energy from the mutated
residue K152 contributed to drug compared to those of R152 in wildtype
were found to be a primary source of high-level of oseltamivir
resistance due to the R152K mutation.
Abstract: The effects of chitosan, a biodegradable polymer,
were studied in Grammatophyllum speciosum protocorm-like bodies
(PLBs) in vitro culture. The chitosan concentration of 0, 5, 10, 15,
20, 25, 50 or 100 mg/l were supplemented in half-strength Murashige
and Skoog (1/2 MS) liquid or on agar media containing 2% (w/v)
sucrose. The results showed that liquid medium supplemented with
15 mg/l chitosan showed the highest relative growth rate (7-fold
increase) of PLBs. On 1/2 MS agar medium supplemented with 25
mg/l chitosan gave the highest relative growth rate (4-fold increase).
The relative growth rate of G. speciosum PLBs on agar medium was
significantly lower than that in liquid medium. Moreover, chitosan,
supplemented to agar medium promoted shoot formation but not
rooting. However, supplementation at too high a level, such as 100
mg/l can inhibit growth and kill PLBs.
Abstract: Malate dehydrogenase-glutamate oxaloacetate
aminotransferase (MDh-GOAT) enzyme complex (the EC) was
isolated and purified from wheat and rise, their some main physicchemical
properties were studied. Michael-s constants of the EC
MDh-GOAT to malate, glutamate and NAD were investigated. This
kinetic results show a high relationship to glutamate. Taking into
account important role of the the EC in catabolism of glutamate – the
central amino acid of a nitric exchange, there is a sharp necessity of
deeper studying of this enzyme complex. Therefore the basic purpose
of the work is studying the basic physical and chemical properties of
this enzyme complex discovered by us, which would be very
important for understanding the mechanisms of reaction catalyzed by
the EC.
Abstract: Protein and Esterase electrophoresis were used to
genetically identify two Saudi tick species. Engorged females of the
camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the
cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks
collected from infested camels and cattle in the animals resting
house at Hail region in KSA were used. The results showed that
there are a variation in both of protein and esterase activity levels and
a high polymorphism within and between the genera and species of
Hyalomma and Boophilus . In conclusion, the protein and esterase
electrophoretic analysis used in the present study could successfully
distinguish among tick species, commonly found in Saudi Arabia.
Abstract: This study aims to screen out and to optimize the
major nutrients for maximum carotenoid production and
antioxidation characteristics by Rhodotorula rubra. It was found that
supplementary of 10 g/l glucose as carbon source, 1 g/l ammonium
sulfate as nitrogen source and 1 g/l yeast extract as growth factor in
the medium provided the better yield of carotenoid content of 30.39
μg/g cell dry weight the amount of antioxidation of Rhodotorula
rubra by DPPH, ABTS and MDA method were 1.463%, 34.21% and
34.09 μmol/l, respectively.
Abstract: EcoDam is an adenine-N6 DNA methyltransferase
that methylates the GATC sites in the Escherichia coli genome.
DNA-adenine methylation is not present in higher eukaryotes
including humans. These observations raise the possibility that dam
inhibitors may be used as anti-microbial agents. Polyphosphate
(Poly(P)) is an important metabolite and signaling molecule in
prokaryotes and eukaryotes. Here, by using gel retardation
experiments to investigate the competition of DNA binding by
EcoDam in the presence of polyphosphate, we found that Poly (P)
strongly interferes with DNA binding by EcoDam, while same
concentration of monophosphate does not. In addition, we
demonstrated that Poly (P) binding inhibits the activity of EcoDam
and our results suggest that Poly (P) led to strong inhibition of the
EcoDam catalytic activity, while monophosphate had only moderate
effect.