Abstract: Morphogenesis is the process that underpins the selforganised development and regeneration of biological systems. The ability to mimick morphogenesis in artificial systems has great potential for many engineering applications, including production of biological tissue, design of robust electronic systems and the co-ordination of parallel computing. Previous attempts to mimick these complex dynamics within artificial systems have relied upon the use of evolutionary algorithms that have limited their size and complexity. This paper will present some insight into the underlying dynamics of morphogenesis, then show how to, without the assistance of evolutionary algorithms, design cellular architectures that converge to complex patterns.
Abstract: Agropyron cristatum L. Gaertn. is a native grass of
semiarid region in Iran which is quit resistant to cool and drought
climate and withstand heavy grazing. This species has close
phylogenetic relationship with Triticum and Hordeum. In this
research, the effect of seven different concentrations of growth
regulator 2,4-D on callus production and somatic embryogenesis of
A. cristatum was investigated on Murashige and Skoog medium. The
results showed that the rate of callus, embryo and neomorph were
highest in 1 mg L-1 2,4-D. Callus production was increased in 1 mg
L-1 2,4-D but dramatically decreased at 5.5 and 9 mg L-1 2,4-D. The
somatic embryos were observed at 1 and 4 mg L-1 2,4-D but matured
embryos and plantlet were only occurred at 1 mg L-1 2,4-D. There
were significant differences between 1 mg L-1 2,4-D and other
treatments for producing globular and torpedo embryos, plantlet,
rooted callus and number of roots (p
Abstract: The Constraints imposed by non-thermal
leptogenesis on the survival of the neutrino mass models describing
the presently available neutrino mass patterns, are studied
numerically. We consider the Majorana CP violating phases coming
from right-handed Majorana mass matrices to estimate the baryon
asymmetry of the universe, for different neutrino mass models
namely quasi-degenerate, inverted hierarchical and normal
hierarchical models, with tribimaximal mixings. Considering two
possible diagonal forms of Dirac neutrino mass matrix as either
charged lepton or up-quark mass matrix, the heavy right-handed
mass matrices are constructed from the light neutrino mass matrix.
Only the normal hierarchical model leads to the best predictions of
baryon asymmetry of the universe, consistent with observations in
non-thermal leptogenesis scenario.
Abstract: The sequential morphologic changes of rabbit duodenal mucosa-submucosa were studied from primodial stage to birth in 15 fetuses and during the early days of life in 21 rabbit newborns till maturity using light, scanning and transmission electron microscopy. Fetal rabbit duodenum develops from a simple tube of stratified epithelium to a tube containing villus and intervillus regions of simple columnar epithelium. By day 21 of gestation, the first rudimentary villi were appeared and by day 24 the first true villi were appeared. The Crypts of Lieberkuhn did not appear until birth. By the first day of postnatal life the duodenal glands appeared. The histological maturity of the rabbit small intestine occurred one month after birth. In conclusion, at all stages, the sequential morphologic changes of the rabbit small intestine developed to meet the structural and physiological demands during the fetal stage to be prepared to extra uterine life.
Abstract: Segmentation, filtering out of measurement errors and
identification of breakpoints are integral parts of any analysis of
microarray data for the detection of copy number variation (CNV).
Existing algorithms designed for these tasks have had some successes
in the past, but they tend to be O(N2) in either computation time or
memory requirement, or both, and the rapid advance of microarray
resolution has practically rendered such algorithms useless. Here we
propose an algorithm, SAD, that is much faster and much less thirsty
for memory – O(N) in both computation time and memory requirement
-- and offers higher accuracy. The two key ingredients of SAD are the
fundamental assumption in statistics that measurement errors are
normally distributed and the mathematical relation that the product of
two Gaussians is another Gaussian (function). We have produced a
computer program for analyzing CNV based on SAD. In addition to
being fast and small it offers two important features: quantitative
statistics for predictions and, with only two user-decided parameters,
ease of use. Its speed shows little dependence on genomic profile.
Running on an average modern computer, it completes CNV analyses
for a 262 thousand-probe array in ~1 second and a 1.8 million-probe
array in 9 seconds
Abstract: MiRNAs participate in gene regulation of translation.
Some studies have investigated the interactions between genes and
intragenic miRNAs. It is important to study the miRNA binding sites
of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid
programmes were used to compute the hybridization free
energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%,
and 39.7% of miRNA binding sites were present in the 5'UTRs,
CDSs, and 3'UTRs, respectively. The density of the binding sites for
miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to
8.0 times greater than in the CDS and 3'UTR, respectively. Three
types of miRNA interactions with mRNAs have been revealed: 5'-
dominant canonical, 3'-compensatory, and complementary binding
sites. MiRNAs regulate gene expression, and information on the
interactions between miRNAs and mRNAs could be useful in
molecular medicine. We recommend that newly described sites
undergo validation by experimental investigation.
Abstract: Novel polystrene-bound Schiff bases and their Pt(IV)
complexes have been prepared from condensation reaction of
polystyrene-A-NH2 with 2-hydroxybenzaldehyde and 5-fluoro-3-
bromo-2-hydroxybenzaldehyde. The structures of Pt(IV) complexes
with polystyrene including Schiff bases have been determined by
elemental analyses, magnetic susceptibility, IR, 1H-NMR, UV-vis,
TG/DTA and AAS. The antibacterial and antifungal activities of the
synthesized compounds have been studied by the well-diffusion
method against some selected microorganisms: (Bacillus cereus spp.,
Listeria monocytogenes 4b, Micrococcus luteus, Staphylococcus
aureus, Staphylococcus epidermis, Brucella abortus, Escherichia
coli, Pseudomonas putida spp., Shigella dysenteria type 10,
Salmonella typhi H).
Abstract: The conventional GA combined with a local search
algorithm, such as the 2-OPT, forms a hybrid genetic algorithm(HGA)
for the traveling salesman problem (TSP). However, the geometric
properties which are problem specific knowledge can be used to
improve the search process of the HGA. Some tour segments (edges)
of TSPs are fine while some maybe too long to appear in a short tour.
This knowledge could constrain GAs to work out with fine tour
segments without considering long tour segments as often.
Consequently, a new algorithm is proposed, called intelligent-OPT
hybrid genetic algorithm (IOHGA), to improve the GA and the 2-OPT
algorithm in order to reduce the search time for the optimal solution.
Based on the geometric properties, all the tour segments are assigned
2-level priorities to distinguish between good and bad genes. A
simulation study was conducted to evaluate the performance of the
IOHGA. The experimental results indicate that in general the IOHGA
could obtain near-optimal solutions with less time and better accuracy
than the hybrid genetic algorithm with simulated annealing algorithm
(HGA(SA)).
Abstract: Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.
Abstract: This study evaluated the microbiological quality
and the sensory characteristics of carp fillets processed by the
sousvide method when stored at 2 and 10 °C. Four different
combinations of sauced–storage were studied then stored at 2 or 10
°C was evaluate periodically sensory, microbiological and
chemical quality. Batches stored at 2 °C had lower growth rates of
mesophiles and psychrotrophs. Moreover, these counts decreased
by increasing the heating temperature and time. Staphylococcus
aureus, Bacillus cereus, Clostridium perfringens and Listeria
monocytogenes were not found in any of the samples. The heat
treatment of 90 °C for 15 min and sauced was the most effective to
ensure the safety and extend the shelf-life of sousvide carp
preserving its sensory characteristics. This study establishes the
microbiological quality of sous vide carp and emphasizes the
relevance of the raw materials, heat treatment and storage
temperature to ensure the safety of the product.
Abstract: Pyritisation halos are identified in weathering crusts and unconsolidated formations at five locations within large fault structure of the Urals’ eastern slope. Electron microscopy reveals the presence of inclusions and growths on pyrite faces – normally on cubic pyrite with striations, or combinations of cubes and other forms. Following neogenesis types are established: native elements and intermetallic compounds (including gold and silver), halogenides, sulphides, sulfosalts, tellurides, sulphotellurides,
selenides, tungstates, sulphates, phosphates, carbon-based substances. Direct relationship is noted between amount and diversity of such mineral phases, and proximity to and scale of ore-grade mineralization. Gold and silver, both in native form and within tellurides, presence of lead (galena, native lead), native tungsten, and, possibly, molybdenite and sulfosalts can indicate gold-bearing formations. First find of native tungsten in the Urals is for the first time – in crystallised and druse-like form. Link is suggested between unusual mineralization and “reducing” hydrothermal fluids from deep-seated faults at later stages of Urals’ reactivation.
Abstract: DNA microarray technology is widely used by
geneticists to diagnose or treat diseases through gene expression.
This technology is based on the hybridization of a tissue-s DNA
sequence into a substrate and the further analysis of the image
formed by the thousands of genes in the DNA as green, red or yellow
spots. The process of DNA microarray image analysis involves
finding the location of the spots and the quantification of the
expression level of these. In this paper, a tool to perform DNA
microarray image analysis is presented, including a spot addressing
method based on the image projections, the spot segmentation
through contour based segmentation and the extraction of relevant
information due to gene expression.
Abstract: Biclustering is a very useful data mining technique for
identifying patterns where different genes are co-related based on a
subset of conditions in gene expression analysis. Association rules
mining is an efficient approach to achieve biclustering as in
BIMODULE algorithm but it is sensitive to the value given to its
input parameters and the discretization procedure used in the
preprocessing step, also when noise is present, classical association
rules miners discover multiple small fragments of the true bicluster,
but miss the true bicluster itself. This paper formally presents a
generalized noise tolerant bicluster model, termed as μBicluster. An
iterative algorithm termed as BIDENS based on the proposed model
is introduced that can discover a set of k possibly overlapping
biclusters simultaneously. Our model uses a more flexible method to
partition the dimensions to preserve meaningful and significant
biclusters. The proposed algorithm allows discovering biclusters that
hard to be discovered by BIMODULE. Experimental study on yeast,
human gene expression data and several artificial datasets shows that
our algorithm offers substantial improvements over several
previously proposed biclustering algorithms.
Abstract: The article presents test results on the changes
occurring in sewage sludge during the process of its storage. Tests
were conducted on mechanically dehydrated sewage sludge derived
from large municipal sewage treatment plants equipped with
biological sewage treatment systems. In testing presented in the paper
the focus was on the basic fuel properties of sewage sludge: moisture
content, heat of combustion, carbon share. In the first part of the
article the overview of the issues concerning the sewage sludge
management is presented and the genesis of tests is explained.
Further in the paper, selected results of conducted tests are discussed.
Changes in tested parameters were determined in the period of a 10-
month sewage storage.
Abstract: The gustatory system allows animals to distinguish
varieties of food and affects greatly the consumption of food, hence
the health and growth of animals. In the current study, we
investigated the histogenesis of vallate papillae (VLP) in the rabbit
tongue using light and scanning electron microscopy. Samples were
obtained from rabbit embryos at the embryonic days 16-30 (E16-30),
and from newborns until maturity; 6 months. At E16, the first
primordia of vallate papillae were observed as small pits on the
surface epithelium of the tongue-s root. At E18, the caudal part was
prominent with loose mesenchymal tissue core; meanwhile the rostral
part of the papilla was remained as a thick mass of epithelial cells. At
E20-24, the side epithelium formed the primitive annular groove. At
E26, the primitive taste buds appeared only at the papillary surface
and reached their maturity by E28. The annular groove started to
appear at E26 became more defined at E28. The definitive vallate
papillae with substantial number of apparently mature taste buds
were observed by the end of the second week. We conclude that the
vallate papillae develop early and mature during the early postnatal
life.
Abstract: There is strong evidence that water channel proteins
'aquaporins (AQPs)' are central components in plant-water relations
as well as a number of other physiological parameters. We had
previously reported the isolation of 24 plasma membrane intrinsic
protein (PIP) type AQPs. However, the gene numbers in rice and the
polyploid nature of bread wheat indicated a high probability of
further genes in the latter. The present work focused on identification
of further AQP isoforms in bread wheat. With the use of altered
primer design, we identified five genes homologous, designated
PIP1;5b, PIP2;9b, TaPIP2;2, TaPIP2;2a, TaPIP2;2b. Sequence
alignments indicate PIP1;5b, PIP2;9b are likely to be homeologues of
two previously reported genes while the other three are new genes
and could be homeologs of each other. The results indicate further
AQP diversity in wheat and the sequence data will enable physical
mapping of these genes to identify their genomes as well as genetic to
determine their association with any quantitative trait loci (QTLs)
associated with plant-water relation such as salinity or drought
tolerance.
Abstract: The treatment of the industrial wastewater can be
particularly difficult in the presence of toxic compounds. Excessive
concentration of Chromium in soluble form is toxic to a wide variety
of living organisms. Biological removal of heavy metals using natural
and genetically engineered microorganisms has aroused great interest
because of its lower impact on the environment. Ralston
metallidurans, formerly known as Alcaligenes eutrophus is a LProteobacterium
colonizing industrial wastewater with a high content
of heavy metals. Tris-buffered mineral salt medium was used for
growing Alcaligenes eutrophus AE104 (pEBZ141). The cells were
cultivated for 18 h at 30 oC in Tris-buffered mineral salt medium
containing 3 mM disodium sulphate and 46 mM sodium gluconate as
the carbon source. The cells were harvested by centrifugation,
washed, and suspended in 10 mM Tris HCl, pH 7.0, containing 46
mM sodium gluconate, and 5 mM Chromium. Interaction among
induction of chr resistance determinant, and chromate reduction have
been demonstrated. Results of this study show that the above bacteria
can be very useful for bioremediation of chromium from industrial
wastewater.
Abstract: The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.
Abstract: Epstein-Barr virus (EBV) is implicated in the pathogenesis of the endemic Burkitt-s lymphoma (BL). The EBVpositive BL-derived cell lines initially maintain the original tumor phenotype of EBV infection (latency I, LatI), but most of them drift toward a lymphoblast phenotype of EBV latency III (LatIII) during in vitro culturing. The aim of the present work was to characterize the B-cell subsets in EBV-positive BL cell lines and to verify whether a particular cell subset correlates with the type of EBV infection. The phenotype analysis of two EBV-negative and eleven EBV-positive (three of LatI and eight of LatIII) BL cell lines was performed by polychromatic flow cytomery, based on expression pattern of CD19, CD10, CD38, CD27, and CD5 markers. Two cell subsets, CD19+CD10+ and CD19+CD10-, were defined in LatIII BL cell lines. In both subsets, the CD27 and CD5 cell surface expression was detected in a proportion of the cells.
Abstract: For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new
sequence features, the frameshift sensitivity (FS) and the accumulative
penta-mer complexity (APC), were discovered which
were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments
were performed on six model organisms to test the power
of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons
and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have
great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.