International Journal of Biological, Life and Agricultural Sciences

SIMGraph: Simplifying Contig Graph to Improve de Novo Genome Assembly Using Next-generation Sequencing Data

Year: 2012 Volume: 6 Issue: 7 435 - 440 Pages

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.

Effect of Cassava Root Ensiled with Cassava Top or Legumes on Feed Intake and Digestibility of Dairy Cows

Year: 2013 Volume: 7 Issue: 1 13 - 15 Pages

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.

Determination of Penicillins Residues in Livestock and Marine Products by LC/MS/MS

Year: 2011 Volume: 5 Issue: 9 517 - 519 Pages

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.

Poverty Alleviation Potential of Snail Farming in Ondo State, Southwest Nigeria

Year: 2010 Volume: 4 Issue: 12 889 - 893 Pages

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.

Investigation on Polymer Based Nano-Silver as Food Packaging Materials

Year: 2013 Volume: 7 Issue: 12 1096 - 1102 Pages

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.

In vitro Plant Regeneration of Java Vetiver (Vetiveria zizanioides)

Year: 2013 Volume: 7 Issue: 9 833 - 835 Pages

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.

Effect of Rollers Differential Speed and Paddy Moisture Content on Performance of Rubber Roll Husker

Year: 2010 Volume: 4 Issue: 11 802 - 805 Pages

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

Synthesis of Sterile and Pyrogen Free Biogenic Magnetic Nanoparticles: Biotechnological Potential of Magnetotactic Bacteria for Production of Nanomaterials

Year: 2013 Volume: 7 Issue: 2 98 - 102 Pages

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.

Interspecific Variation in Heat Stress Tolerance and Oxidative Damage among 15 C3 Species

Year: 2012 Volume: 6 Issue: 11 1000 - 1003 Pages

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.

Effect of Ginger and L-Carnitine on the Reproductive Performance of Male Rats

Year: 2012 Volume: 6 Issue: 4 137 - 143 Pages

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.

Effect of Humic Acid on Physical and Engineering Properties of Lime-Treated Organic Clay

Year: 2011 Volume: 5 Issue: 11 651 - 656 Pages

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.

A Software Framework for Predicting Oil-Palm Yield from Climate Data

Year: 2007 Volume: 1 Issue: 11 140 - 145 Pages

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.

Heritability Estimates of Lactation Traits in Maltese Goat

Year: 2011 Volume: 5 Issue: 6 335 - 337 Pages

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.

A Comparison of Fuel Usage and Harvest Capacity in Self-Propelled Forage Harvesters

Year: 2013 Volume: 7 Issue: 7 504 - 509 Pages

Authors:
Brian H. Marsh

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.

Determination of Cr Content in Canned Fish Marketed in Iran

Year: 2014 Volume: 8 Issue: 12 1310 - 1313 Pages

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.

Vocal Communication in Sooty-headed Bulbul; Pycnonotus aurigaster

Year: 2012 Volume: 6 Issue: 4 131 - 136 Pages

Authors:
Surakan Payakkhabut

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.

Effect of Heat-Moisture Treatment on the Formation and Properties of Resistant Starches From Mung Bean (Phaseolus radiatus) Starches

Year: 2010 Volume: 4 Issue: 12 881 - 888 Pages

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.

In Silico Analysis of Pax6 Interacting Proteins Indicates Missing Molecular Links in Development of Brain and Associated Disease

Year: 2009 Volume: 3 Issue: 12 555 - 561 Pages

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.

SAF: A Substitution and Alignment Free Similarity Measure for Protein Sequences

Year: 2008 Volume: 2 Issue: 8 147 - 155 Pages

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.

The Tyrosinase and Cyclooxygenase Inhibitory Activities and Cytotoxicity Screening of Tamarindus indica Seeds

Year: 2013 Volume: 7 Issue: 1 10 - 12 Pages

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.