Abstract: Mammalian genomes contain large number of
retroelements (SINEs, LINEs and LTRs) which could affect
expression of protein coding genes through associated transcription
factor binding sites (TFBS). Activity of the retroelement-associated
TFBS in many genes is confirmed experimentally but their global
functional impact remains unclear. Human SINEs (Alu repeats) and
mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich
gene rich genome segments consistent with the view that they
can contribute to regulation of gene expression. We have shown
earlier that Alu are involved in formation of cis-regulatory modules
(clusters of TFBS) in human promoters, and other authors reported
that Alu located near promoter CpG islands have an increased
frequency of CpG dinucleotides suggesting that these Alu are
undermethylated. Human Alu and mouse B1/B2 elements have an
internal bipartite promoter for RNA polymerase III containing
conserved sequence motif called B-box which can bind basal
transcription complex TFIIIC. It has been recently shown that TFIIIC
binding to B-box leads to formation of a boundary which limits
spread of repressive chromatin modifications in S. pombe. SINEassociated
B-boxes may have similar function but conservation of
TFIIIC binding sites in SINEs located near mammalian promoters
has not been studied earlier. Here we analysed abundance and
distribution of retroelements (SINEs, LINEs and LTRs) in annotated
sequences of the Database of mammalian transcription start sites
(DBTSS). Fractions of SINEs in human and mouse promoters are
slightly lower than in all genome but >40% of human and mouse
promoters contain Alu or B1/B2 elements within -1000 to +200 bp
interval relative to transcription start site (TSS). Most of these SINEs
is associated with distal segments of promoters (-1000 to -200 bp
relative to TSS) indicating that their insertion at distances >200 bp
upstream of TSS is tolerated during evolution. Distribution of SINEs
in promoters correlates negatively with the distribution of CpG
sequences. Using analysis of abundance of 12-mer motifs from the
B1 and Alu consensus sequences in genome and DBTSS it has been
confirmed that some subsegments of Alu and B1 elements are poorly
conserved which depends in part on the presence of CpG
dinucleotides. One of these CpG-containing subsegments in B1
elements overlaps with SINE-associated B-box and it shows better
conservation in DBTSS compared to genomic sequences. It has been
also studied conservation in DBTSS and genome of the B-box
containing segments of old (AluJ, AluS) and young (AluY) Alu
repeats and found that CpG sequence of the B-box of old Alu is
better conserved in DBTSS than in genome. This indicates that Bbox-
associated CpGs in promoters are better protected from
methylation and mutation than B-box-associated CpGs in genomic
SINEs. These results are consistent with the view that potential
TFIIIC binding motifs in SINEs associated with human and mouse
promoters may be functionally important. These motifs may protect
promoters from repressive histone modifications which spread from
adjacent sequences. This can potentially explain well known
clustering of SINEs in GC-rich gene rich genome compartments and
existence of unmethylated CpG islands.
Abstract: 15 strains of oil-destructing microorganisms were
isolated from oil polluted soil of Western Kazakhstan. Strains 2-A
and 41-3 with the highest oil-destructing activities were chosen from
them. It was shown that these strains oxidized n-alkanes very well,
but isoalkanes, isoparaffin, cycloparaffin and heavy aromatic
compounds were destructed very slowly. These both strains were
tested as preparations for bioremediation of oil-polluted soil in model
and field experiments. The degree of utilizing of soil oil by this
preparation was 79-84 % in field experiments.
Abstract: New biostimulator from wheat seeds which by its
chemical composition relates to fusicoccin is presented in this article.
New biostimulator could be used as powerful hormonal substance
that has ability to increase productivity and salt tolerance of
agricultural plants. Also on the basis of biostimulator we have
developed vegetative method for fast reproduction of perennial plants
as desert plant - Tamarix gracilis.
Abstract: Article devoted to the development of technologies
for medicine and agroecology by using plant organelle – spherosome.
Technological method of purification and isolation of this organelle
by using novel nanostructured carbon sorbent – “nanocarbosorb"
ARK type are presented. Also the methods of preparation of
nanocontainers based on using of spherosome with loaded isosorbide
dinitrate, piroxicam or diclofenak are exhibited. We found that the
spherosome could be applied for ecological aims as bioregulator and
also as biosensor for determination of ammonia ions in water
reservoirs at concentration range 1mM to 100mM.
Abstract: Electrocardiogram (ECG) segmentation is necessary
to help reduce the time consuming task of manually annotating
ECG-s. Several algorithms have been developed to segment the ECG
automatically. We first review several of such methods, and then
present a new single lead segmentation method based on Adaptive
piecewise constant approximation (APCA) and Piecewise derivative
dynamic time warping (PDDTW). The results are tested on the QT
database. We compared our results to Laguna-s two lead method. Our
proposed approach has a comparable mean error, but yields a slightly
higher standard deviation than Laguna-s method.
Abstract: A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.
Abstract: Migration in breast cancer cell wound healing assay
had been studied using image fractal dimension analysis. The
migration of MDA-MB-231 cells (highly motile) in a wound healing
assay was captured using time-lapse phase contrast video microscopy
and compared to MDA-MB-468 cell migration (moderately motile).
The Higuchi fractal method was used to compute the fractal
dimension of the image intensity fluctuation along a single pixel
width region parallel to the wound. The near-wound region fractal
dimension was found to decrease three times faster in the MDA-MB-
231 cells initially as compared to the less cancerous MDA-MB-468
cells. The inner region fractal dimension was found to be fairly
constant for both cell types in time and suggests a wound influence
range of about 15 cell layer. The box-counting fractal dimension
method was also used to study region of interest (ROI). The MDAMB-
468 ROI area fractal dimension was found to decrease
continuously up to 7 hours. The MDA-MB-231 ROI area fractal
dimension was found to increase and is consistent with the behavior
of a HGF-treated MDA-MB-231 wound healing assay posted in the
public domain. A fractal dimension based capacity index has been
formulated to quantify the invasiveness of the MDA-MB-231 cells in
the perpendicular-to-wound direction. Our results suggest that image
intensity fluctuation fractal dimension analysis can be used as a tool
to quantify cell migration in terms of cancer severity and treatment
responses.
Abstract: In this paper we introduce the notion of protein interaction
network. This is a graph whose vertices are the protein-s
amino acids and whose edges are the interactions between them.
Using a graph theory approach, we identify a number of properties of
these networks. We compare them to the general small-world network
model and we analyze their hierarchical structure.
Abstract: The literature reports a large number of approaches for
measuring the similarity between protein sequences. Most of these
approaches estimate this similarity using alignment-based techniques
that do not necessarily yield biologically plausible results, for two
reasons.
First, for the case of non-alignable (i.e., not yet definitively aligned
and biologically approved) sequences such as multi-domain, circular
permutation and tandem repeat protein sequences, alignment-based
approaches do not succeed in producing biologically plausible results.
This is due to the nature of the alignment, which is based on the
matching of subsequences in equivalent positions, while non-alignable
proteins often have similar and conserved domains in non-equivalent
positions.
Second, the alignment-based approaches lead to similarity measures
that depend heavily on the parameters set by the user for the alignment
(e.g., gap penalties and substitution matrices). For easily alignable
protein sequences, it's possible to supply a suitable combination of
input parameters that allows such an approach to yield biologically
plausible results. However, for difficult-to-align protein sequences,
supplying different combinations of input parameters yields different
results. Such variable results create ambiguities and complicate the
similarity measurement task.
To overcome these drawbacks, this paper describes a novel and
effective approach for measuring the similarity between protein
sequences, called SAF for Substitution and Alignment Free. Without
resorting either to the alignment of protein sequences or to substitution
relations between amino acids, SAF is able to efficiently detect the
significant subsequences that best represent the intrinsic properties of
protein sequences, those underlying the chronological dependencies of
structural features and biochemical activities of protein sequences.
Moreover, by using a new efficient subsequence matching scheme,
SAF more efficiently handles protein sequences that contain similar
structural features with significant meaning in chronologically
non-equivalent positions. To show the effectiveness of SAF, extensive
experiments were performed on protein datasets from different
databases, and the results were compared with those obtained by
several mainstream algorithms.
Abstract: Health problems linked to urban growth are current
major concerns of developing countries. In 2002 and 2005, an
interdisciplinary program “Populations et Espaces ├á Risques
SANitaires" (PERSAN) was set up under the patronage of the
Development and Research Institute. Centered on health in
Cameroon-s urban environment, the program mainly sought to (i)
identify diarrhoea risk factors in Yaoundé, (ii) to measure their
prevalence and apprehend their spatial distribution. The crosssectional
epidemiological study that was carried out revealed a
diarrheic prevalence of 14.4% (437 cases of diarrhoea on the 3,034
children examined). Also, among risk factors studied, household
refuse management methods used by city dwellers were statistically
associated to these diarrhoeas. Moreover, it happened that levels of
diarrhoeal attacks varied consistently from one neighbourhood to
another because of the discrepancy urbanization process of the
Yaoundé metropolis.
Abstract: The microbiological and physicochemical
characteristics of wetland soils in Eket Local Government Area were
studied between May 2001 and June 2003. Total heterotrophic
bacterial counts (THBC), total fungal counts (TFC), and total
actinomycetes counts (TAC) were determined from soil samples
taken from four locations at two depths in the wet and dry seasons.
Microbial isolates were characterized and identified. Particle size and
chemical parameters were also determined using standard methods.
THBC ranged from 5.2 (+0.17) x106 to 1.7 (+0.18) x107 cfu/g and
from 2.4 (+0.02) x106 to 1.4 (+0.04) x107cfu/g in the wet and dry
seasons, respectively. TFC ranged from 1.8 (+0.03) x106 to 6.6 (+
0.18) x106 cfu/g and from 1.0 (+0.04) x106 to 4.2 (+ 0.01) x106 cfu/g
in the wet and dry seasons, respectively .TAC ranged from 1.2
(+0.53) x106 to 6.0 (+0.05) x106 cfu/g and from 0.6 (+0.01) x106 to
3.2 (+ 0.12) x106 cfu/g in the wet and dry season, respectively.
Acinetobacter, Alcaligenes, Arthrobacter, Bacillus, Beijerinckja,
Enterobacter, Micrococcus, Flavobacterium, Serratia, Enterococcus,
and Pseudomonas species were predominant bacteria while
Aspergillus, Fusarium, Mucor, Penicillium, and Rhizopus were the
dominant fungal genera isolated. Streptomyces and Norcadia were
the actinomycetes genera isolated. The particle size analysis showed
high sand fraction but low silt and clay. The pH and % organic
matter were generally acidic and low, respectively at all locations.
Calcium dominated the exchangeable bases with low electrical
conductivity and micronutrients. These results provide the baseline
data of Eket wetland soils for its management for sustainable
agriculture.