Abstract: De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.
Abstract: The effect of cassava root ensiled with cassava top or
legumes on voluntary feed intake and milk production were
determined in 12 dairy cows using a 4×3 change-over design.
Experimental period were 30 days long and consisted of 14 days of
adaptation. Silage was prepared from cassava root mixed with
cassava top or legumes at ratio 60:40. Cows were allotted at random
to receive ad libitum one of four rations: T1) control, T2) cassava
root +cassava top-silages, T3) cassava root +hamata - silages and T4)
cassava root +Thapra stylo-silages.
The dry matter intake (BW0.75) was higher (P< 0.05) in cow fed
with silages diets compared with T1. However, the intake of T2 was
higher among treatments. Milk production was lowest in cow fed
with T1. Among silages based diets, milk production was not
significantly different but 4%FCM was higher in cow fed T2. Milk
compositions were not affected by feeding diets.
It is concluded that feeding cassava root ensiled with its leaves as
a supplement increased dry matter intake and significantly improved
4%FCM. The combination of cassava root and legume silages did not
improve the feed intake but did increase the milk production.
Abstract: Multi-residue analysis method for penicillins was
developed and validated in bovine muscle, chicken, milk, and flatfish.
Detection was based on liquid chromatography tandem mass
spectrometry (LC/MS/MS). The developed method was validated for
specificity, precision, recovery, and linearity. The analytes were
extracted with 80% acetonitrile and clean-up by a single
reversed-phase solid-phase extraction step. Six penicillins presented
recoveries higher than 76% with the exception of Amoxicillin
(59.7%). Relative standard deviations (RSDs) were not more than
10%. LOQs values ranged from 0.1 and to 4.5 ug/kg. The method was
applied to 128 real samples. Benzylpenicillin was detected in 15
samples and Cloxacillin was detected in 7 samples. Oxacillin was
detected in 2 samples. But the detected levels were under the MRL
levels for penicillins in samples.
Abstract: The recurring decimal of rural and urban poverty in
Nigeria, resulting from lack of sustainable livelihood activities by
the people due to non-diversification of the economy, necessitated
this study. One hundred snail farmers were randomly selected in
Akure North and Akure South Local Government areas of Ondo
State, Southwest Nigeria where snail farming is widely practised.
Data collection was through questionnaires administration and onsite
observation of farms. Data obtained were subjected to
descriptive statistics, Student-s t-test and regression analysis. Cost
benefit ratio (CBR) and rate of return on investment (RORI) were
calculated in order to determine the poverty alleviation potentials of
snail farming in the study areas. Although snail farming was
profitable and viable, it was below poverty line. With time and more
knowledge in its farming activities, and with more people taking to
snail production, its poverty alleviation and reduction potentials will
increase.
Abstract: Commercial nanocomposite food packaging type nano-silver containers were characterised using scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). The presence of nanoparticles consistent with the incorporation of 1% nano-silver (Ag) and 0.1% titanium dioxide (TiO2) nanoparticle into polymeric materials formed into food containers was confirmed. Both nanomaterials used in this type of packaging appear to be embedded in a layered configuration within the bulk polymer. The dimensions of the incorporated nanoparticles were investigated using X-ray diffraction (XRD) and determined by calculation using the Scherrer Formula; these were consistent with Ag and TiO2 nanoparticles in the size range 20-70nm both were spherical shape nanoparticles. Antimicrobial assessment of the nanocomposite container has also been performed and the results confirm the antimicrobial activity of Ag and TiO2 nanoparticles in food packaging containers. Migration assessments were performed in a wide range of food matrices to determine the migration of nanoparticles from the packages. The analysis was based upon the relevant European safety Directives and involved the application of inductively coupled plasma mass spectrometry (ICP-MS) to identify the range of migration risk. The data pertain to insignificance levels of migration of Ag and TiO2 nanoparticles into the selected food matrices.
Abstract: In vitro plant regeneration has been successfully obtained from basal shoot explant of Vetiveria zizanioides through indirect organogenesis. The explant was cultured in Murashige & Skoog’s (MS) media supplemented with 2,4-D, IAA, and kinetin in various concentrations. Callus was well induced in media supplemented with 2 ppm 2,4-D, 1 ppm IAA, and 1 ppm kinetin. This callus was then transferred to MS media supplemented with 1 - 5 ppm of BAP for shoot regeneration. The media supplemented with 3 ppm BAP was a suitable medium for shoot induction, as well as for shoot multiplication. Rooting was well developed in shoot following transferred to half MS media containing 0.2 ppm IBA. Plantlet was then transferred to husk charcoal for acclimatization, and almost all (90%) of plantlets were survived during acclimatization.
Abstract: A study was carried out at the Rice Research Institute of Iran (RRII) to investigate the effect of rollers differential peripheral speed of commercial rubber roll husker and paddy moisture content on the husking index and percentage of broken rice. The experiment was conducted at six levels of rollers differential speed (1.5, 2.2, 2.9, 3.6, 4.3 and 5 m/s) and three levels of paddy moisture content (8-9, 10-11 and 12-13% w.b.). Two common paddy varieties namely, Binam and Khazer, were selected for this study. Results revealed that the effect of rollers differential speed and moisture content significantly (P
Abstract: Today, biogenic magnetite nanoparticles among
magnetic nanoparticles have unique attracted attention because of
their magnetic characteristics and potential applications in various
fields such as therapeutic and diagnostic. A well known example of
these biogenic nanoparticles is magnetosomes of magnetotactic
bacteria. In this research, we used two different types of technique for
the isolation and purification of magnetosome nanoparticles from the
isolated magnetotactic bacterial cells, heat-alkaline treatment and
sonication. Also we evaluated pyrogen content and sterility of
synthesized the isolated individual magnetosome by the Limulus
Amoebocyte Lysate test and direct impedimetric method
respectively.
Abstract: The C3 plants are frequently suffering from exposure
to high temperature stress which limits the growth and yield of these
plants. This study seeks to clarify the physiological mechanisms of
heat tolerance in relation to oxidative stress in C3 species. Fifteen C3
species were exposed to prolonged moderately high temperature
stress 36/30°C for 40 days in a growth chamber. Chlorophyll
fluorescence (Fv/Fm) showed great difference among species at 40
days of the stress. The species showed decreases in Fv/Fm and
increases in malondialdehyde (MDA) content under stress condition
as well as negative correlation between Fv/Fm and MDA (r = -0.61*)
at 40 days of the stress. Hydrogen peroxide (H2O2) content before
and after stress in addition to its response under stress showed great
differences among species. The results suggest that the difference in
heat tolerance among C3 species is closely associated with the ability
to suppress oxidative damage but not with the content of reactive
oxygen species (ROS) which is regulated by complex network.
Abstract: In this study, we investigated the effects of ginger and
L-carnitine on the reproductive performance of male rats with respect
to semen parameters, male sex hormones and the testicular
antioxidant system. A total of sixty mature male albino rats were
divided into four groups of fifteen rats. The control group received
saline, whereas the other three groups received ginger (100 mg kg-1 d-
1.), L-carnitine (150 mg kg-1 d-1.) or a combination of both ginger
(100 mg kg-1 d-1.) and L-carnitine (150 mg kg-1 d-1.) via a stomach
tube daily for one month. At the end of the treatment period, the rats
were sacrificed, and their sperm characteristics (count, motility and
viability), antioxidant enzyme factors levels (reduced glutathione,
catalase, superoxide dismutase and total antioxidant capacity) and sex
hormone levels (testosterone, Follicle stimulating hormone(FSH) and
luteinizing hormone (LH) were analysed. Our results showed that the
three experimental treatments improved sperm parameters,
antioxidant enzyme activity and testosterone hormone levels; the
most pronounced positive effects were observed in the group that
received a combination of both ginger and L-carnitine. Therefore, the
administration of a combination of ginger and L-carnitine may be
beneficial for improving male sexual performance.
Abstract: The present work deals with the stabilisation of
organic clay using hydrated lime. Artificial organic clays were
prepared by adding kaolin and different humic acid contents. Results
given by physical testing show that the presence of humic acid has a
drawback effect on the untreated organic clay. The decrease in
specific gravity value was accompanied by a decrease in dry density
and plasticity of clay at higher humic acid contents. Significant
increase in shear strength at 7 days of curing period is observed in the
lime-treated samples up to 5% lime content. However shear strength
of lime-treated organic clay decreases at longer curing periods. The
results given by laboratory testing is further verified by
microstructure analysis. Based on the results obtained in this study, it
can be concluded that the presence of more than 1.5% humic acid
reduces significantly the efficiency of lime stabilization in organic
clays.
Abstract: Intelligent systems based on machine learning
techniques, such as classification, clustering, are gaining wide spread
popularity in real world applications. This paper presents work on
developing a software system for predicting crop yield, for example
oil-palm yield, from climate and plantation data. At the core of our
system is a method for unsupervised partitioning of data for finding
spatio-temporal patterns in climate data using kernel methods which
offer strength to deal with complex data. This work gets inspiration
from the notion that a non-linear data transformation into some high
dimensional feature space increases the possibility of linear
separability of the patterns in the transformed space. Therefore, it
simplifies exploration of the associated structure in the data. Kernel
methods implicitly perform a non-linear mapping of the input data
into a high dimensional feature space by replacing the inner products
with an appropriate positive definite function. In this paper we
present a robust weighted kernel k-means algorithm incorporating
spatial constraints for clustering the data. The proposed algorithm
can effectively handle noise, outliers and auto-correlation in the
spatial data, for effective and efficient data analysis by exploring
patterns and structures in the data, and thus can be used for
predicting oil-palm yield by analyzing various factors affecting the
yield.
Abstract: Data on 657 lactation from 163 Maltese goat,
collected over a 5-year period were analyzed by a mixed model to
estimate the variance components for heritability. The considered
lactation traits were: milk yield (MY) and lactation length (LL). Year,
parity and type of birth (single or twin) were significant sources of
variation for lactation length; on the other hand milk yield was
significantly influenced only by the year. The average MY was
352.34 kg and the average LL was 230 days. Estimates of heritability
were 0.21 and 0.15 for MY and LL respectively. These values
suggest there is low correlation between genotype and phenotype so
it may be difficult to evaluate animals directly on phenotype. So, the
genetic improvement of this breed may be quite slow without the
support of progeny test aimed to select Maltese breeders.
Abstract: Self-propelled forage harvesters in the 850
horsepower range were tested over three years for fuel consumption,
throughput and quality of chop for corn silage. Cut length had a
significant effect on fuel consumption, throughput and some aspects
of chop quality. Measure cut length was often different than
theoretical length of cut. Where cut length was equivalent fuel
consumption and throughput were equivalent across brands.
Shortening cut length from 17 to 11mm increases fuel consumption
53 percent measured as Mg of silage harvested per gallon of fuel used
and a 42 percent decrease in capacity as tons of fresh material per
hour run time.
Abstract: The presence of heavy metals in the environment
could constitute a hazard to food security and public health. These
can be accumulated in aquatic animals such as fish. Samples of four
popular brands of canned fish in the Iranian market (yellowfin tuna,
common Kilka, Kawakawa and longtail tuna) were analyzed for level
of Cr after wet digestion with acids using graphite furnace atomic
absorption spectrophotometry. The mean concentrations for Cr in the
different brands were: 2.57, 3.24, 3.16 and 1.65 μg/g for brands A, B,
C and D respectively. Significant differences were observed in the Cr
levels between all of the different brands of canned fish evaluated in
this study. The Cr concentrations for the varieties of canned fishes
were generally within the FAO/WHO, U.S. FDA and U.S. EPA
recommended limits for fish.
Abstract: Studies of vocal communication in Sooty-headed
Bulbul were carried out from January to December 2011. Vocal
recordings and behavioral observations were made in their natural
habitats at some localities of Lampang, Thailand. After editing, cuts
of high quality recordings were analyzed with the help of Avisoft-
SASLab Pro (version 4.40) software. More than one thousand
element repertoires in five groups were found within two vocal
structures. The two structures were short sounds with single element
and phrases composed of elements, the frequency ranged from 1-10
kHz. Most phrases were composed of 2 to 5 elements that were often
dissimilar in structure, however, these phrases were not as complex
as song phrases. The elements and phrases were combined to form
many patterns. The species used ten types of calls; i.e. alert, alarm,
aggressive, begging, contact, courtship, distress, exciting, flying and
invitation. Alert and contact calls were used more frequently than
other calls. Aggressive, alarm and distress calls could be used for
interspecific communication among some other bird species in the
same habitats.
Abstract: Mung bean starches were subjected to heat-moisture treatment (HMT) by different moisture contents (15%, 20%, 25%, 30% and 35%) at 120Ôäâ for 12h. The impact on the yields of resistant starch (RS), microstructure, physicochemical and functional properties was investigated. Compared to native starch, the RS content of heat-moisture treated starches increased significantly. The RS level of HMT-20 was the highest of all the starches. Birefringence was displayed clear at the center of native starch. For HMT starches, pronounced birefringence was exhibited on the periphery of starch granules; however, birefringence disappeared at the centre of some starch granules. The shape of HMT starches hadn-t been changed and the integrity of starch granules was preserved for all the conditions. Concavity could be observed on HMT starches under scanning electronic microscopy. After HMT, apparent amylose contents were increased and starch macromolecule was degraded in comparison with those of native starch. There was a reduction in swelling power on HMT starches, but the solubility of HMT starches was higher than that of native starch. Both of native and HMT starches showed A-type X-ray diffraction pattern. Furthermore, there is a higher intensity at the peak of 15.0 and 22.9 Å than those of native starch.
Abstract: The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.
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: The methanolic extracts from seeds of tamarind
(Tamarindus indica) was prepared by Soxhlet apparatus extraction
and evaluated for total phenolic content by Folin-Ciocalteu method.
Then, methanolic extract was screened biological activities (In vitro)
for anti-melanogenic activity by tyrosinase inhibition test, antiinflammation
activity by cyclooxygenase 1 (COX-1) and
cyclooxygenase 2 (COX-2) inhibition test, and cytotoxic screening
test with Vero cells. The results showed that total phenolic content,
which contained in extract, was contained 27.72 mg of gallic acid
equivalent per g of dry weight. The ability to inhibit tyrosinase
enzyme, which exerted by Tamarind seed extracts (1 mg/ml) was
52.13 ± 0.42 %. The extract was not possessed inhibitory effect to
COX-1 and COX-2 enzymes and cytotoxic effect to Vero cells. The
finding is concludes that tested seed extract was possessed
antimelanogenic activity with non-toxic effects. However, there was
not exhibited anti-inflammatory activity. Further studies include the
use of advance biological models to confirm this biological activity,
as well as, the isolation and characterization of the purified
compounds that it was contained.