Abstract: Bioinformatics and computational biology involve
the use of techniques including applied mathematics,
informatics, statistics, computer science, artificial intelligence,
chemistry, and biochemistry to solve biological problems
usually on the molecular level. Research in computational
biology often overlaps with systems biology. Major research
efforts in the field include sequence alignment, gene finding,
genome assembly, protein structure alignment, protein structure
prediction, prediction of gene expression and proteinprotein
interactions, and the modeling of evolution. Various
global rearrangements of permutations, such as reversals and
transpositions,have recently become of interest because of their
applications in computational molecular biology. A reversal is
an operation that reverses the order of a substring of a permutation.
A transposition is an operation that swaps two adjacent
substrings of a permutation. The problem of determining the
smallest number of reversals required to transform a given
permutation into the identity permutation is called sorting by
reversals. Similar problems can be defined for transpositions
and other global rearrangements. In this work we perform a
study about some genome rearrangement primitives. We show
how a genome is modelled by a permutation, introduce some
of the existing primitives and the lower and upper bounds
on them. We then provide a comparison of the introduced
primitives.
Abstract: Characterized as rich mineral substances, low
temperature, few bacteria, and stability with numerous implementation
aspects on aquaculture, food, drinking, and leisure, the deep sea water
(DSW) development has become a new industry in the world. It has
been report that marine algae contain various biologically active
compounds. This research focued on the affections in cultivating
Sagrassum cristaefolium with different concentration of deep sea
water(DSW) and surface sea water(SSW). After two and four weeks,
the total phenolic contents were compared in Sagrassum cristaefolium
culturing with different ways, and the reductive activity of them was
also be tried with potassium ferricyanide. Those fresh seaweeds were
dried with oven and were ground to powder. Progressively, the marine
algae we cultured was extracted by water under the condition with
heating them at 90Ôäâ for 1hr.The total phenolic contents were be
executed using Folin–Ciocalteu method. The results were explaining
as follows: the highest total phenolic contents and the best reductive
ability of all could be observed on the 1/4 proportion of DSW to SSW
culturing in two weeks. Furthermore, the 1/2 proportion of DSW to
SSW also showed good reductive ability and plentiful phenolic
compositions. Finally, we confirmed that difference proportion of
DSW and SSW is the major point relating to ether the total phenolic
components or the reductive ability in the Sagrassum cristaefolium. In
the future, we will use this way to mass production the marine algae or
other micro algae on industry applications.
Abstract: There is an ongoing controversy in the literature related
to the biological effects of weak, low frequency electromagnetic
fields. The physical arguments and interpretation of the experimental
evidence are inconsistent, where some physical arguments and
experimental demonstrations tend to reject the likelihood of any
effect of the fields at extremely low level. The problem arises of
explaining, how the low-energy influences of weak magnetic fields
can compete with the thermal and electrical noise of cells at normal
temperature using the theoretical studies. The magnetoreception in
animals involve radical pair mechanism. The same mechanism has
been shown to be involved in the circadian rhythm synchronization in
mammals. These reactions can be influenced by the weak magnetic
fields. Hence, it is postulated the biological clock can be affected
by weak magnetic fields and these disruptions to the rhythm can
cause adverse biological effects. In this paper, likelihood of altering
the biological clock via the radical pair mechanism is analyzed to
simplify these studies of controversy.
Abstract: Approximate tandem repeats in a genomic sequence are
two or more contiguous, similar copies of a pattern of nucleotides.
They are used in DNA mapping, studying molecular evolution
mechanisms, forensic analysis and research in diagnosis of inherited
diseases. All their functions are still investigated and not well
defined, but increasing biological databases together with tools for
identification of these repeats may lead to discovery of their specific
role or correlation with particular features. This paper presents a new
approach for finding approximate tandem repeats in a given sequence,
where the similarity between consecutive repeats is measured using
the Hamming distance. It is an enhancement of a method for finding
exact tandem repeats in DNA sequences based on the Burrows-
Wheeler transform.
Abstract: The research focuses on the effects of polyphenols
extracted from Sambucus nigra fruit, using an experimental arterial
hypertension pattern, as well as their influence on the oxidative
stress. The results reveal the normalization of the reduced glutathion
concentration, as well as a considerable reduction in the
malondialdehide serum concentration by the polyphenolic protection.
The rat blood pressure values were recorded using a CODATM
system, which uses a non-invasive blood pressure measuring method.
All the measured blood pressure components revealed a biostatistically
significant (p
Abstract: Microbubbbles incorporating ultrasound have been used to increase the efficacy of targeted drug delivery, because microstreaming induced by cavitating bubbles affects the drug perfusion into the target cells and tissues. In order to clarify the physical effects of microstreaming on drug perfusion into tissues, a preliminary experimental study of perfusion enhancement by a stably oscillating microbubble was performed. Microstreaming was induced by an oscillating bubble at 15 kHz, and perfusion of dye into an agar phantom was optically measured by histology on agar phantom. Surface color intensity and the penetration length of dye in the agar phantom were increased more than 70% and 30%, respectively, due to the microstreaming induced by an oscillating bubble. The mass of dye perfused into a tissue phantom for 30 s was increased about 80% in the phantom with an oscillating bubble. This preliminary experiment shows the physical effects of steady streaming by an oscillating bubble can enhance the drug perfusion into the tissues while minimizing the biological effects.
Abstract: There is an urgent need to conserve the biological diversity of the Nigerian Environment for the future and present generation in the face of current energy resources development. This paper gives an in-depth analysis of the impact of oil and gas activities on the biological diversity of the Nigerian Niger Delta area and its consequences on the sustainable development of the host communities as it relates to their social, economic and environmental issues, particularly on the womenfolk who are the key managers of environmental resources. Also reviewed is the frustration of these communities that is reflected in unending conflicts.
Abstract: Bionanotechnology deals with nanoscopic interactions between nanostructured materials and biological systems. Polymer nanocomposites with optimized biological activity have attracted great attention. Nanoclay is considered as reinforcing nanofiller in manufacturing of high performance nanocomposites. In current study, organomodified-nanoclay with negatively charged silicate layers was incorporated into biomedical grade silicone rubber. Nanoparticle loading has been tailored to enhance cell behavior. Addition of nanoparticles led to improved mechanical properties of substrate with enhanced strength and stiffness while no toxic effects was observed. Results indicated improved viability and proliferation of cells by addition of nanofillers. The improved mechanical properties of the matrix result in proper cell response through adjustment and arrangement of cytoskeletal fibers. Results can be applied in tissue engineering when enhanced substrates are required for improvement of cell behavior for in vivo applications.
Abstract: Nigella sativa L. is an aromatic plant belonging to the
family Ranunculaceae. It has been used traditionally, especially in the
middle East and India, for the treatment of asthma, cough, bronchitis,
headache, rheumatism, fever, influenza and eczema. Several
biological activities have been reported in Nigella sativa seeds,
including antioxidant. In this context we tried to estimate the
antioxidant activity of various extracts prepared from Nigella sativa
seeds, methanolic extract (ME), chloroformic extract (CE), hexanic
extract (HE : fixed oil), ethyl acetate extract (EAE) water extract
(WE). The Folin-Ciocalteu assay showed that CE and EAE contained
high level of phenolic compounds 81.31 and 72.43μg GAE/mg of
extract respectively. Similarly, the CE and EAE exhibited the highest
DPPH radical scavenging activity, with IC50 values of 106.56μg/ml
and 121.62μg/ml respectively. In addition, CE and HE showed the
most scavenging activity against superoxide radical generated in the
PMS-NADH-NBT system with respective IC50 values of 361.86
μg/ml and 371.80 μg/ml, which is comparable to the activity of the
standard antioxidant BHT (344.59 μg/ml). Ferrous ion chelating
capacity assay showed that WE, EAE and ME are the most active
with 40.57, 39.70 and 22.02 mg EDTA-E/g of extract. The inhibition
of linoleic acid/ß-carotene coupled oxidation was estimated by ßcarotene
bleaching assay, this showed a highest relative antioxidant
activity with CE and EAE (69.82% of inhibition). The antioxidant
activities of the methanolic extract and the fixed oil are confirmed by
an in vivo assay in mice, the daily oral administration of methanolic
extract (500 and 800 mg/kg/day) and fixed oil (2 and 4 ml/kg/day)
during 21 days, resulted in a significant enhancement of the blood
total antioxidant capacity (measured by KRL test) and the plasmatic
antioxidant capacity towards DPPH radical.
Abstract: Three batches of yogurts were made with soy protein
isolate (SPI) supplemented with 2% (S2), 4% (S4) or 6% (S6) of
skim milk powder (SMP). The fourth batch (control; S0) was
prepared from SPI without SMP supplementation. Lactobacillus
delbrueckii ssp. bulgaricus ATCC 11842 (Lb 11842) and
Streptococcus thermophilus ST 1342 (ST 1342) were used as the
starter culture. Biotransformation of the inactive forms, isoflavone
glycosides (IG) to biologically active forms, isoflavone aglycones
(IA), was determined during 28 d storage. The viability of both
microorganisms was significantly higher (P < 0.05) in S2, S4, and S6
than that in S0. The ratio of lactic acid/acetic acid in S0 was in the
range of 15.53 – 22.31 compared to 7.24 – 12.81 in S2, S4 and S6.
The biotransformation of IG to IA in S2, S4 and S6 was also
enhanced by 9.9 -13.3% compared to S0.
Abstract: The role of the pollen grain, with to the reproductive
process of higher plants, is to deliver the spermatic cells to the
embryo sac for egg fertilization. The aim of this project was study
the effect of electromagnetic fields on structure and pollen grains
development in Chenopodium album. Anthers of Chenopodium
album L. were collected at different stages of development from
control (without electromagnetic field) and plants grown at 10m from
the field sources. Structure and development of pollen grains were
studied and compared. The studying pollen structure by Light and
Scanning electron microscopy showed that electromagnetic fields
reduction of pollen grains number and male sterility, thus , in some
anthers, pollen grains were attached together and deformed compared
to control ones. The data presented suggest that prolonged exposures
of plants to magnetic field may cause different biological effects at
the cellular tissue and organ levels.
Abstract: Silicon is a beneficial element for plant growth. It
helps plants to overcome multiple stresses, alleviates metal toxicity
and improves nutrient imbalance. Field experiment was conducted as
split-split plot arranged in a randomized complete block design with
four replications. Irrigation system include continues flooding and
deficit as main plots and nitrogen rates N0, N46, N92, and N138 kg/ha
as sub plots and silicon rates Si0 & Si500 kg/ha as sub-subplots.
Results indicate that grain yield had not significant difference
between irrigation systems. Flooding irrigation had higher biological
yield than deficit irrigation whereas, no significant difference in grain
and straw yield. Nitrogen application increased grain, biological and
straw yield. Silicon application increased grain, biological and straw
yield but, decreased harvest index. Flooding irrigation had higher
number of total tillers / hill than deficit irrigation, but deficit
irrigation had higher number of fertile tillers / hill than flooding
irrigation. Silicon increased number of filled spikelet and decreased
blank spikelet. With high nitrogen application decreased 1000-grain
weight. It can be concluded that if the nitrogen application was high
and water supplied was available we could have silicon application
until increase grain yield.
Abstract: The field of biomedical materials plays an imperative
requisite and a critical role in manufacturing a variety of biological
artificial replacements in a modern world. Recently, titanium (Ti)
materials are being used as biomaterials because of their superior
corrosion resistance and tremendous specific strength, free- allergic
problems and the greatest biocompatibility compared to other
competing biomaterials such as stainless steel, Co-Cr alloys,
ceramics, polymers, and composite materials. However, regardless of
these excellent performance properties, Implantable Ti materials have
poor shear strength and wear resistance which limited their
applications as biomaterials. Even though the wear properties of Ti
alloys has revealed some improvements, the crucial effectiveness of
biomedical Ti alloys as wear components requires a comprehensive
deep understanding of the wear reasons, mechanisms, and techniques
that can be used to improve wear behavior. This review examines
current information on the effect of thermal and thermomechanical
processing of implantable Ti materials on the long-term prosthetic
requirement which related with wear behavior. This paper focuses
mainly on the evolution, evaluation and development of effective
microstructural features that can improve wear properties of bio
grade Ti materials using thermal and thermomechanical treatments.
Abstract: Recently, nanomaterials are developed in the form of nano-films, nano-crystals and nano-pores. Lanthanide phosphates as a material find extensive application as laser, ceramic, sensor, phosphor, and also in optoelectronics, medical and biological labels, solar cells and light sources. Among the different kinds of rare-earth orthophosphates, yttrium orthophosphate has been shown to be an efficient host lattice for rare earth activator ions, which have become a research focus because of their important role in the field of light display systems, lasers, and optoelectronic devices. It is in this context that the 4fn- « 4fn-1 5d transitions of rare earth in insulating materials, lying in the UV and VUV, are the aim of large number of studies .Though there has been a few reports on Eu3+, Nd3+, Pr3+,Er3+, Ce3+, Tm3+ doped YPO4. The 4fn- « 4fn-1 5d transitions of the rare earth dependent to the host-matrix, several matrices ions were used to study these transitions, in this work we are suggesting to study on a very specific class of inorganic material that are orthophosphate doped with rare earth ions. This study focused on the effect of Ce3+ concentration on the structural and optical properties of Ce3+ doped YPO4 yttrium orthophosphate with powder form prepared by the Sol Gel method.
Abstract: Data mining incorporates a group of statistical
methods used to analyze a set of information, or a data set. It operates
with models and algorithms, which are powerful tools with the great
potential. They can help people to understand the patterns in certain
chunk of information so it is obvious that the data mining tools have
a wide area of applications. For example in the theoretical chemistry
data mining tools can be used to predict moleculeproperties or
improve computer-assisted drug design. Classification analysis is one
of the major data mining methodologies. The aim of thecontribution
is to create a classification model, which would be able to deal with a
huge data set with high accuracy. For this purpose logistic regression,
Bayesian logistic regression and random forest models were built
using R software. TheBayesian logistic regression in Latent GOLD
software was created as well. These classification methods belong to
supervised learning methods.
It was necessary to reduce data matrix dimension before construct
models and thus the factor analysis (FA) was used. Those models
were applied to predict the biological activity of molecules, potential
new drug candidates.
Abstract: PDMS (Polydimethylsiloxane) polymer is a suitable material for biological and MEMS (Microelectromechanical systems) designers, because of its biocompatibility, transparency and high resistance under plasma treatment. PDMS round channel is always been of great interest due to its ability to confine the liquid with membrane type micro valves. In this paper we are presenting a very simple way to form round shapemicrofluidic channel, which is based on reflow of positive photoresist AZ® 40 XT. With this method, it is possible to obtain channel of different height simply by varying the spin coating parameters of photoresist.
Abstract: With the rapid development in the field of life
sciences and the flooding of genomic information, the need for faster
and scalable searching methods has become urgent. One of the
approaches that were investigated is indexing. The indexing methods
have been categorized into three categories which are the lengthbased
index algorithms, transformation-based algorithms and mixed
techniques-based algorithms. In this research, we focused on the
transformation based methods. We embedded the N-gram method
into the transformation-based method to build an inverted index
table. We then applied the parallel methods to speed up the index
building time and to reduce the overall retrieval time when querying
the genomic database. Our experiments show that the use of N-Gram
transformation algorithm is an economical solution; it saves time and
space too. The result shows that the size of the index is smaller than
the size of the dataset when the size of N-Gram is 5 and 6. The
parallel N-Gram transformation algorithm-s results indicate that the
uses of parallel programming with large dataset are promising which
can be improved further.
Abstract: Biological Ammonia removal (nitrification), the
oxidation of ammonia to nitrate catalyzed by bacteria, is a key part of
global nitrogen cycling. In the first step of nitrification,
chemolithoautotrophic ammonia oxidizer transform ammonia to
nitrite, this subsequently oxidized to nitrate by nitrite oxidizing
bacteria. This process can be affected by several factors. In this study
the effect of influent COD on biological ammonia removal in a
bench-scale biological reactor was investigated. Experiments were
carried out using synthetic wastewater. The initial ammonium
concentration was 25mgNH4
+-N L-1. The effect of COD between
247.55±1.8 and 601.08±3.24mgL-1 on biological ammonia removal
was investigated by varying the COD loading supplied to reactor.
From the results obtained in this study it could be concluded in the
range of 247.55±1.8 to 351.35±2.05mgL-1, there is a direct
relationship between amount of COD and ammonia removal.
However more than 351.35±2.05 up to 601.08±3.24mgL-1 were
found an indirect relationship between them.
Abstract: In order to evaluation the effects of soil organic
matter and biofertilizer on chickpea quality and biological
nitrogen fixation, field experiments were carried out in 2007
and 2008 growing seasons. In this research the effects of
different strategies for soil fertilization were investigated on
grain yield and yield component, minerals, organic compounds
and cooking time of chickpea. Experimental units were
arranged in split-split plots based on randomized complete
blocks with three replications. Main plots consisted of (G1):
establishing a mixed vegetation of Vicia panunica and
Hordeum vulgare and (G2): control, as green manure levels.
Also, five strategies for obtaining the base fertilizer
requirement including (N1): 20 t.ha-1 farmyard manure; (N2):
10 t.ha-1 compost; (N3): 75 kg.ha-1 triple super phosphate;
(N4): 10 t.ha-1 farmyard manure + 5 t.ha-1 compost and (N5):
10 t.ha-1 farmyard manure + 5 t.ha-1 compost + 50 kg.ha-1
triple super phosphate were considered in sub plots.
Furthermoree four levels of biofertilizers consisted of (B1):
Bacillus lentus + Pseudomonas putida; (B2): Trichoderma
harzianum; (B3): Bacillus lentus + Pseudomonas putida +
Trichoderma harzianum; and (B4): control (without
biofertilizers) were arranged in sub-sub plots. Results showed
that integrating biofertilizers (B3) and green manure (G1)
produced the highest grain yield. The highest amounts of yield
were obtained in G1×N5 interaction. Comparison of all 2-way
and 3-way interactions showed that G1N5B3 was determined
as the superior treatment. Significant increasing of N, P2O5,
K2O, Fe and Mg content in leaves and grains emphasized on
superiority of mentioned treatment because each one of these
nutrients has an approved role in chlorophyll synthesis and
photosynthesis abilities of the crops. The combined application
of compost, farmyard manure and chemical phosphorus (N5)
in addition to having the highest yield, had the best grain
quality due to high protein, starch and total sugar contents, low
crude fiber and reduced cooking time.
Abstract: Spatial trends are one of the valuable patterns in geo
databases. They play an important role in data analysis and
knowledge discovery from spatial data. A spatial trend is a regular
change of one or more non spatial attributes when spatially moving
away from a start object. Spatial trend detection is a graph search
problem therefore heuristic methods can be good solution. Artificial
immune system (AIS) is a special method for searching and
optimizing. AIS is a novel evolutionary paradigm inspired by the
biological immune system. The models based on immune system
principles, such as the clonal selection theory, the immune network
model or the negative selection algorithm, have been finding
increasing applications in fields of science and engineering.
In this paper, we develop a novel immunological algorithm based
on clonal selection algorithm (CSA) for spatial trend detection. We
are created neighborhood graph and neighborhood path, then select
spatial trends that their affinity is high for antibody. In an
evolutionary process with artificial immune algorithm, affinity of
low trends is increased with mutation until stop condition is satisfied.