Abstract: In the paper, the relative performances on spectral
classification of short exon and intron sequences of the human and
eleven model organisms is studied. In the simulations, all
combinations of sixteen one-sequence numerical representations, four
threshold values, and four window lengths are considered. Sequences
of 150-base length are chosen and for each organism, a total of
16,000 sequences are used for training and testing. Results indicate
that an appropriate combination of one-sequence numerical
representation, threshold value, and window length is essential for
arriving at top spectral classification results. For fixed-length
sequences, the precisions on exon and intron classification obtained
for different organisms are not the same because of their genomic
differences. In general, precision increases as sequence length
increases.
Abstract: Recent years have seen a growing trend towards the
integration of multiple information sources to support large-scale
prediction of protein-protein interaction (PPI) networks in model
organisms. Despite advances in computational approaches, the
combination of multiple “omic" datasets representing the same type
of data, e.g. different gene expression datasets, has not been
rigorously studied. Furthermore, there is a need to further investigate
the inference capability of powerful approaches, such as fullyconnected
Bayesian networks, in the context of the prediction of PPI
networks. This paper addresses these limitations by proposing a
Bayesian approach to integrate multiple datasets, some of which
encode the same type of “omic" data to support the identification of
PPI networks. The case study reported involved the combination of
three gene expression datasets relevant to human heart failure (HF).
In comparison with two traditional methods, Naive Bayesian and
maximum likelihood ratio approaches, the proposed technique can
accurately identify known PPI and can be applied to infer potentially
novel interactions.
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: Vermiculite was used to develop inorganic
carrier-based formulations of fluorescent pseudomonad strains
R62 and R81. The effect of bio-inoculation of fluorescent
pseudomonad strains R62 and R81 (plant growth promoting
and biocontrol agent) on growth responses of Vigna-mungo
under field condition was enumerated. The combined bioinoculation
of these two organisms in a formuation increased
the pods yield by 300% in comparison to the control crop.
There was also significant increment in the other plant growth
responses such as dry root weight, dry shoot weight, shoot
length and number of branches per plant.
Abstract: Lactic acid alone and its combined application with
nisin were evaluated for reducing population of naturally occurring
microorganisms on chilled shrimp. Fresh shrimps were dipped in 0,
1.0% and 2.0% (v/v) lactic acid alone and their combined application
with 0.04 (g/L/kg) nisin solution for 10 min. Total plate counts of
aerobic bacteria (TPCs), Psychrotrophic counts, population of
Pseudomonas spp., H2S producing bacteria and Lactic acid bacteria
(LAB) on shrimps were determined during storage at 4 °C. The
results indicated that total plate counts were 2.91 and 2.63 log CFU/g
higher on untreated shrimps after 7 and 14 days of storage,
respectively, than on shrimps treated with 2.0% lactic acid combined
with 0.04 (g/L/kg) nisin. Both concentrations of lactic acid indicated
significant reduction on Pseudomonas counts during storage, while
2.0% lactic acid combined with nisin indicated the highest reduction.
In addition, H2S producing bacteria were more sensitive to high
concentration of lactic acid combined with nisin during storage.
Abstract: Compared to oil production from microorganisms, little work has been performed for mixed culture of microalgae and yeast. In this article it is aimed to show high oil accumulation potential of mixed culture of microalgae Chlorella sp. KKU-S2 and oleaginous yeast Torulaspora maleeae Y30 using sugarcane molasses as substrate. The monoculture of T. maleeae Y30 grew faster than that of microalgae Chlorella sp. KKU-S2. In monoculture of yeast, a biomass of 6.4g/L with specific growth rate (m) of 0.265 (1/d) and lipid yield of 0.466g/L were obtained, while 2.53g/L of biomass with m of 0.133 (1/d) and lipid yield of 0.132g/L were obtained for monoculture of Chlorella sp. KKU-S2. The biomass concentration in the mixed culture of T. maleeae Y30 with Chlorella sp. KKU-S2 increased faster and was higher compared with that in the monoculture and mixed culture of microalgae. In mixed culture of microalgae Chlorella sp. KKU-S2 and C. vulgaris TISTR8580, a biomass of 3.47g/L and lipid yield of 0.123 g/L were obtained. In mixed culture of T. maleeae Y30 with Chlorella sp. KKU-S2, a maximum biomass of 7.33 g/L and lipid yield of 0.808g/L were obtained. Maximum cell yield coefficient (YX/S, 0.229g/L), specific yield of lipid (YP/X, 0.11g lipid/g cells) and volumetric lipid production rate (QP, 0.115 g/L/d) were obtained in mixed culture of yeast and microalgae. Clearly, T. maleeae Y30 and Chlorella sp. KKU-S2 use sugarcane molasses as organic nutrients efficiently in mixed culture under mixotrophic growth. The biomass productivity and lipid yield are notably enhanced in comparison with monoculture.
Abstract: Abstract–The objectives of the current study are to determine the
prevalence, etiological agents, drug susceptibility pattern and plasmid
profile of Acinetobacter baumannii isolates from Hospital-Acquired
Infections (HAI) at Community Hospital, Al Jouf Province, Saudi
Arabia. A total of 1890 patients had developed infection during
hospital admission and were included in the study. Among those who
developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had
respiratory tract infection (RTI), blood stream infections (BSI) and
urinary tract (UTI) respectively. A total of 268 bacterial isolates were
isolated from nosocomial infection. S. aureus was reported in 23.5%
for of the total isolates followed by Klebsiella pneumoniae (17.5%), E.
coli (17.2%), P. aeruginosa (11.9%), coagulase negative
staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp.
(3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and
Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated
organisms are multi-drug resistant, predominantly Gram-positive
pathogens with a high incidence of methicillin-resistant S. aureus,
extended spectrum beta lactamase and vancomycin resistant
enterococci organisms. The RFLP (Fragment Length Polymorphisms)
patterns of plasmid preparations from isolated A. baumannii isolates
had altered RFLP patterns, possibly due to the presence of plasmid(s).
Five A. baumannii isolates harbored plasmids all of which were not
less than 2.71kbp in molecular weight. Hence, it showed that the gene
coding for the isolates were located on the plasmid DNA while the
remaining isolates which have no plasmid might showed gene coding
for antibiotic resistance being located on chromosomal DNA.
Nosocomial infections represent a current problem in Community
Hospital, Al Jouf Province, Saudi Arabia. Problems associated with
SSI include infection with multidrug resistant pathogens which are
difficult to treat and are associated with increased mortality.
Abstract: In recent years application of natural antimicrobials
instead of conventional ones, due to their hazardous effects on health,
has got serious attentions. On the basis of the results of different
studies, chitosan, a natural bio-degradable and non-toxic
biopolysaccharide derived from chitin, has potential to be used as a
natural antimicrobial. Chitosan has exhibited high antimicrobial
activity against a wide variety of pathogenic and spoilage
microorganisms, including fungi, and Gram-positive and Gramnegative
bacteria. The antimicrobial action is influenced by intrinsic
factors such as the type of chitosan, the degree of chitosan
polymerization and extrinsic factors such as the microbial organism,
the environmental conditions and presence of the other components.
The use of chitosan in food systems should be based on sufficient
knowledge of the complex mechanisms of its antimicrobial mode of
action. In this article we review a number of studies on the
investigation of chitosan antimicrobial properties and application of
them in culture and food mediums.
Abstract: Pentachlorophenol (PCP) is a polychlorinated
aromatic compound that is widespread in industrial effluents and is
considered to be a serious pollutant. Among the variety of industrial
effluents encountered, effluents from tanning industry are very
important and have a serious pollution potential. PCP is also formed
unintentionally in effluents of paper and pulp industries. It is highly
persistent in soils and is lethal to a wide variety of beneficial
microorganisms and insects, human beings and animals. The natural
processes that breakdown toxic chemicals in the environment have
become the focus of much attention to develop safe and environmentfriendly
deactivation technologies. Microbes and plants are among
the most important biological agents that remove and degrade waste
materials to enable their recycling in the environment. The present
investigation was carried out with the aim of developing a microbial
system for bioremediation of PCP polluted soils. A number of plant
species were evaluated for their ability to tolerate different
concentrations of pentachlorophenol (PCP) in the soil. The
experiment was conducted for 30 days under pot culture conditions.
The toxic effect of PCP on plants was studied by monitoring seed
germination, plant growth and biomass. As the concentration of PCP
was increased to 50 ppm, the inhibition of seed germination, plant
growth and biomass was also increased. Although PCP had a
negative effect on all plant species tested, maize and groundnut
showed the maximum tolerance to PCP. Other tolerating crops
included wheat, safflower, sunflower, and soybean. From the
rhizosphere soil of the tolerant seedlings, as many as twenty seven
PCP tolerant bacteria were isolated. From soybean, 8; sunflower, 3;
safflower 8; maize 2; groundnut and wheat, 3 each isolates were
made. They were screened for their PCP degradation potentials.
HPLC analyses of PCP degradation revealed that the isolate MAZ-2
degraded PCP completely. The isolate MAZ-1 was the next best
isolate with 90 per cent PCP degradation. These strains hold promise
to be used in the bioremediation of PCP polluted soils.
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: Acid rain occurs when sulphur dioxide (SO2) and
nitrogen oxides (Nox) gases react in the atmosphere with water,
oxygen, and other chemicals to form various acidic compounds. The
result is a mild solution of sulfuric acid and nitric acid. Soil has a
greater buffering capacity than aquatic systems. However excessive
amount of acids introduced by acid rains may disturb the entire soil
chemistry. Acidity and harmful action of toxic elements damage
vegetation while susceptible microbial species are eliminated. In
present study, the effects of simulated sulphuric acid and nitric acid
rains were investigated on crop Glycine max. The effect of acid rain
on change in soil fertility was detected in which pH of control sample
was 6.5 and pH of 1%H2SO4 and 1%HNO3 were 3.5. Nitrogen nitrate
in soil was high in 1% HNO3 treated soil & Control sample.
Ammonium nitrogen in soil was low in 1% HNO3 & H2SO4 treated
soil. Ammonium nitrogen was medium in control and other samples.
The effect of acid rain on seed germination on 3rd day of germination
control sample growth was 7 cm, 0.1% HNO3 was 8cm, and 0.001%
HNO3 & 0.001% H2SO4 was 6cm each. On 10th day fungal growth
was observed in 1% and 0.1%H2SO4 concentrations, when all plants
were dead. The effect of acid rain on crop productivity was
investigated on 3rd day roots were developed in plants. On12th day
Glycine max showed more growth in 0.1% HNO3, 0.001% HNO3 and
0.001% H2SO4 treated plants growth were same as compare to control
plants. On 20th day development of discoloration of plant pigments
were observed on acid treated plants leaves. On 38th day, 0.1, 0.001%
HNO3 and 0.1, 0.001% H2SO4 treated plants and control plants were
showing flower growth. On 42th day, acid treated Glycine max variety
and control plants were showed seeds on plants. In Glycine max
variety 0.1, 0.001% H2SO4, 0.1, 0.001% HNO3 treated plants were
dead on 46th day and fungal growth was observed. The toxicological
study was carried out on Glycine max plants exposed to 1% HNO3
cells were damaged more than 1% H2SO4. Leaf sections exposed to
0.001% HNO3 & H2SO4 showed less damaged of cells and
pigmentation observed in entire slide when compare with control
plant. The soil analysis was done to find microorganisms in HNO3 &
H2SO4 treated Glycine max and control plants. No microorganism
growth was observed in 1% HNO3 & H2SO4 but control plant showed
microbial growth.
Abstract: This paper focuses on the experimental impacts of
ultrasonic, carbonate and a combination of them on the quality of
fresh kiwi juice. Today, non-thermal methods like ultrasonic, which
have imperceptible effects on some properties of the juice such as
taste, flavor and color, are commonly used for killing
microorganisms.In this paper, some properties of kiwi fruit juice
under ultrasonic, carbonate and a combination of them has been
researched. Those properties include pH, acidity, transparency and
Brix. Its impact on microorganisms has been studied as well.The
results show that using a combination of carbonate and sonicate make
the cavitation more severe without a perceptible effect on nonactivation
of microorganisms.
Abstract: Phylogenetic tree is a graphical representation of the
evolutionary relationship among three or more genes or organisms.
These trees show relatedness of data sets, species or genes
divergence time and nature of their common ancestors. Quality of a
phylogenetic tree requires parsimony criterion. Various approaches
have been proposed for constructing most parsimonious trees. This
paper is concerned about calculating and optimizing the changes of
state that are needed called Small Parsimony Algorithms. This paper
has proposed enhanced small parsimony algorithm to give better
score based on number of evolutionary changes needed to produce
the observed sequence changes tree and also give the ancestor of the
given input.
Abstract: In composting process, N high-organic wastes loss the
great part of its nitrogen as ammonia; therefore, using compost
amendments can promote the quality of compost due to the decrease
in ammonia volatilization. With regard to the effect of pH on
composting, microorganisms- activity and ammonia volatilization,
sulfuric acid and alkaline wastewater of paper mill (as liming agent
with Ca and Mg ions) were used as compost amendments. Study
results indicated that these amendments are suitable for reclamation
of compost quality properties. These held nitrogen in compost caused
to reduce C/N ratio. Both amendments had a significant effect on
total nitrogen, but it should be used sulfuric acid in fewer amounts
(20 ml/kg fresh organic wastes); and the more amounts of acid is not
proposed.
Abstract: As a result of urbanization, the unpredictable growth of industry and transport, production of chemicals, military activities, etc. the concentration of anthropogenic toxicants spread in nature exceeds all the permissible standards. Most dangerous among these contaminants are organic compounds having great persistence, bioaccumulation, and toxicity along with our awareness of their prominent occurrence in the environment and food chain. Among natural ecological tools, plants still occupying above 40% of the world land, until recently, were considered as organisms having only a limited ecological potential, accumulating in plant biomass and partially volatilizing contaminants of different structure. However, analysis of experimental data of the last two decades revealed the essential role of plants in environment remediation due to ability to carry out intracellular degradation processes leading to partial or complete decomposition of carbon skeleton of different structure contaminants. Though, phytoremediation technologies still are in research and development, their various applications have been successfully used. The paper aims to analyze mechanisms of organic contaminants uptake and detoxification in plants, being the less studied issue in evaluation and exploration of plants potential for environment remediation.
Abstract: This current research focused on development of degradable starch based packaging film with enhanced mechanical properties. A series of low density polyethylene (LDPE)/tapioca starch compounds with various tapioca starch contents were prepared by twin screw extrusion with the addition of maleic anhydride grafted polyethylene as compatibilizer. Palm cooking oil was used as processing aid to ease the blown film process, thus, degradable film can be processed via conventional blown film machine. Studies on their characteristics, mechanical properties and biodegradation were carried out by Fourier Transform Infrared (FTIR) spectroscopy and optical properties, tensile test and exposure to fungi environment respectively. The presence of high starch contents had an adverse effect on the tensile properties of LDPE/tapioca starch blends. However, the addition of compatibilizer to the blends improved the interfacial adhesion between the two materials, hence, improved the tensile properties of the films. High content of starch amount also was found to increase the rate of biodegradability of LDPE/tapioca starch films. It can be proved by exposure of the film to fungi environment. A growth of microbes colony can be seen on the surface of LDPE/tapioca starch film indicates that the granular starch present on the surface of the polymer film is attacked by microorganisms, until most of it is assimilated as a carbon source.
Abstract: Soil microbial activity is adversely affected by pollutants such as heavy metals, antibiotics and pesticides. Organic amendments including sewage sludge, municipal compost and vermicompost are recently used to improve soil structure and fertility. But, these materials contain heavy metals including Pb, Cd, Zn, Ni and Cu that are toxic to soil microorganisms and may lead to occurrence of more tolerant microbes. Among these, Pb is the most abundant and has more negative effect on soil microbial ecology. In this study, Pb levels of 0, 100, 200, 300, 400 and 500 mg Pb [as Pb(NO3)2] per kg soil were added to the pots containing 2 kg of a loamy soil and incubated for 6 months at 25°C with soil moisture of - 0.3 MPa. Dehydrogenase activity of soil as a measure of microbial activity was determined on 15, 30, 90 and 180 days after incubation. Triphenyl tetrazolium chloride (TTC) was used as an electron acceptor in this assay. PICTs (IC50 values) were calculated for each Pb level and incubation time. Soil microbial activity was decreased by increasing Pb level during 30 days of incubation but the induced tolerance appeared on day 90 and thereafter. During 90 to 180 days of incubation, the PICT was gradually developed by increasing Pb level up to 200 mg kg-1, but the rate of enhancement was steeper at higher concentrations.
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: The National Agricultural Biotechnology Information
Center (NABIC) plays a leading role in the biotechnology information
database for agricultural plants in Korea. Since 2002, we have
concentrated on functional genomics of major crops, building an
integrated biotechnology database for agro-biotech information that
focuses on bioinformatics of major agricultural resources such as rice,
Chinese cabbage, and microorganisms. In the NABIC,
integration-based biotechnology database provides useful information
through a user-friendly web interface that allows analysis of genome
infrastructure, multiple plants, microbial resources, and living
modified organisms.
Abstract: Arvia®, a spin-out company of University of Manchester, UK is commercialising a water treatment technology for the removal of low concentrations of organics from water. This technology is based on the adsorption of organics onto graphite based adsorbents coupled with their electrochemical regeneration in a simple electrochemical cell. In this paper, the potential of the process to adsorb microorganisms and electrochemically disinfect them present in water has been demonstrated. Bench scale experiments have indicated that the process of adsorption using graphite adsorbents with electrochemical regeneration can be used for water disinfection effectively. The most likely mechanisms of disinfection of water through this process include direct electrochemical oxidation and electrochemical chlorination.