RAPD analysis of Sclerotium rolfsii isolates causing collar rot of eggplant and tomato

Eight isolates of Sclerotium rolfsii from four strategically geographical sites of Bangladesh were characterized and their cultural properties like average linear mycelial growth, colony colour, colony consistency, growth pattern and sclerotia formation were studied. Isolates varied in mycelial growth and other growth characteristics and were grouped into three. The highest linear growth was displayed by S8. DNA concentration of eight isolates varied from 1150-7200 ng/?l. DNA fingerprinting by RAPD prompted the grouping of isolates. Selected 3 primers generated 20 bands with size ranging from 100-1500 bp. Out of the 20 bands, 9 bands (45%) were polymorphic and 11 bands (55%) were monomorphic among the eight isolates of Sclerotium rolfsii. The co-efficient of gene differentiation (Gst) was 1.000 reflecting the existence of high level of genetic variations among the 8 isolates. The lowest genetic distance and highest inter isolate similarity was found in S1 and S2 which would be homogeneous. The highest genetic distance and lowest inter isolate similarity found in S3, S7 and S3, S8 pair which would be most divergent isolates. The cluster analysis also revealed that S3, S7 and S8 belong to different clusters. All five varieties of eggplant and tomatoes were graded as susceptible when inoculated with eight isolates. Plant mortality 93.33% was recorded in S4, S6 and in S8. Considering the isolate factor the most virulent isolate would be S8 whereas the less virulent isolate would be S2 and S7. Host plant of S8 was tomato collected from Thakurgaon. S2 and S7 were collected from BAU farm and Dinajpur and host plants were lentil and tomato respectively. It is evident that Sclerotium rolfsii from Thakurgaon on host tomato is more virulent.Int. J. Agril. Res. Innov. & Tech. 6 (1): 47-57, June, 201

Simulation of Traffic Flow Model with Traffic Controller Boundary

This paper considers a fluid dynamic traffic flow model appended with a closure linear velocity-density relationship which provides a first order hyperbolic partial differential equation (PDE) and is treated as an initial boundary value problem (IBVP). We consider the boundary value in such a way that one side of highway treat like there is a traffic controller at that point. We present the analytic solution of the traffic flow model as a Cauchy problem. A numerical simulation of the traffic flow model (IBVP) is performed based on a finite difference scheme for the model with two sided boundary conditions and a suitable numerical scheme for this is the Lax-Friedrichs scheme. Solution figure from our scheme indicates a desired result that amplitude and frequency of cars density and velocity reduces as time grows. Also at traffic controller point, velocity and density values change as desired manner. In further, we also want to introduce anisotropic behavior of cars(to get more realistic picture) which has not been considered here. Doi: 10.12777/ijse.5.1.25-30 [How to cite this article: Sultana, N., Parvin, M. , Sarker, R., Andallah, L.S. (2013). Simulation of Traffic Flow Model with Traffic Controller Boundary. International Journal of Science and Engineering, 5(1),25-30. Doi: 10.12777/ijse.5.1.25-30

RNAI MEDIATED GENE SILENCING OF EIF3A: A POSSIBLE SOLUTION TO CONTROL BREAST CANCER

Objective: The eukaryotic translational initiation factor 3A (eIF3A) is reported to be over expressed in most breast cancer cells. In the present study, our aim is to suppress the over expression of eIF3A in human breast cancer MCF-7 cell line using gene silencing technique (RNA interference (RNAi)).Methods: The artificial microRNA (amiRNA) targeting eIF3A gene was constructed by incorporating short interference RNA (siRNA) sequences against eIF3A gene into endogenous microRNA30 (miR-30) and cloned into pcDNA3.1 vector. The amiRNA containing plasmid was then transfected into MCF-7 cell line and the expression of eIF3A was examined by RT-PCR. The cytotoxicity of plasmid with amiRNA targeting eIF3A on MCF–7 cells was evaluated by MTT assay.Results: The amiRNA construct significantly inhibited eIF3A gene expression and reduce the cell viability of MCF-7 cell line.Conclusion: The usage of modified endogenous amiRNA in vector based expression system with significant gene silencing efficiency suggests that RNAi based gene silencing method can be considered as one of the effective means to control cancer.Â

Path Signatures for Seizure Forecasting

Forecasting the state of a system from an observed time series is the subject of research in many domains, such as computational neuroscience. Here, the prediction of epileptic seizures from brain measurements is an unresolved problem. There are neither complete models describing underlying brain dynamics, nor do individual patients exhibit a single seizure onset pattern, which complicates the development of a `one-size-fits-all' solution. Based on a longitudinal patient data set, we address the automated discovery and quantification of statistical features (biomarkers) that can be used to forecast seizures in a patient-specific way. We use existing and novel feature extraction algorithms, in particular the path signature, a recent development in time series analysis. Of particular interest is how this set of complex, nonlinear features performs compared to simpler, linear features on this task. Our inference is based on statistical classification algorithms with in-built subset selection to discern time series with and without an impending seizure while selecting only a small number of relevant features. This study may be seen as a step towards a generalisable pattern recognition pipeline for time series in a broader context

Growth Performance, Carcass Characteristics and Plasma Mineral Chemistry as Affected by Dietary Chloride and Chloride Salts Fed to Broiler Chickens Reared under Phase Feeding System

Requirements of dietary chloride (dCl) and chloride salts were determined by using 4×2 factorial arrangement under four phase feeding program. Four levels (0.31, 0.45, 0.59 and 0.73%) and two sources (NH4Cl and CaCl2) of the dCl were allocated to 1,472 chicks in eight dietary treatments in which each treatment was replicated four times with 46 birds per replicate. The four phase feeding program was comprised of four dietary phases: Prestarter (d 1 to 10), Starter (d 11 to 20), Grower (d 21 to 33) and Finisher (d 34 to 42); and diets were separately prepared for each phase. The cations, anions, pH, dissolved oxygen (DO), temperature, electrical conductivity (EC), total dissolved solids (TDS) and salinity were analyzed in drinking water and were not affected by dietary treatments. BW gain (BWG; p≤0.009) and feed:gain (FG; p≤0.03) were improved in CaCl2 supplemented diets during d 1 to 10. The maximum response of BWG and FG was observed at 0.38% and 0.42% dCl, respectively, for d 34 to 42. However, the level of dCl for BWG during d 21 to 33 (p≤0.04) and d 34 to 42 (p≤0.009) was optimized at 0.60% and 0.42%, respectively. The level of dCl for optimized feed intake (FI; p≤0.006), FG (p≤0.007) and litter moisture (LM; p≤0.001) was observed at 0.60%, 0.38% and 0.73%, respectively, for d 1 to 42. Water intake (DWI) was not affected by increasing dCl supplementation (p>0.05); however, the ratio between DWI and FI (DWI:FI) was found highest at 0.73% dCl during d 1 to 10 (p≤0.05) and d 21 to 33 (p≤0.009). Except for d 34 to 42 (p≤0.006), the increasing level of dCl did not result in a significant difference in mortality during any phase. Blood pH and glucose, and breast and thigh weights (percentage of dressed weight) were improved while dressing percentage (DP) and gastrointestinal health were exacerbated with NH4Cl as compared to CaCl2 supplemented diets (p≤0.001). Higher plasma Na+ and HCO3− and lower Cl− and Ca++ were observed in NH4Cl supplemented diets (p≤0.001). Increasing supplementation of dCl increased plasma Cl− (p≤0.04; quadratically) and linearly reduced plasma K+ (p≤0.001), Ca++ (p≤0.003), HCO3− (p≤0.001), and Na+ (p≤0.001; quadratically). Consequently, higher requirements of dietary chloride are suggested for feed intake; nevertheless, lower levels of dietary chloride are sufficient to support optimal BWG and FG with increasing age. The NH4Cl supplemented diets ameliorate breast and thigh meat yield along with overall energy balance (glucose)

Identification of Fluorescent Compounds with Non-Specific Binding Property via High Throughput Live Cell Microscopy

10.1371/journal.pone.0028802PLoS ONE71

Growth Performance, Carcass Yield, and Quality and Chemical Traits of Meat from Commercial Korean Native Ducks with 2-Way Crossbreeding

This work was conducted to investigate the performance and meat characteristics of commercial Korean native duck (KND). A total of 180 1-d-old ducklings of 2-way crossbreds from A and B lines (from National Institute of Animal Science) were used in this work and divided into 4 groups (3 replicates/group, 15 birds/replicate). The four groups were 4 crossbreds as AA (A line [♀]×A line [♂]), AB (A line [♀]×B line [♂]), BB (Pure line B strains) and BA (B strains [♀]×A strain [♂]). Ducks were fed diets based on corn-soybean meal for 0 to 3 wk (22.4% crude protein [CP], 2,945 kcal/kg metabolizable energy [ME]) and 3 to 8 wk (18.4% CP, 3,047 kcal/kg ME). As a result of this study, average body weight of 4 crossbreds were 625, 1,617, 2,466, and 2,836 g at 2, 4, 6, and 8 weeks, respectively, and significantly increased over the period of time (p<0.05). Body weight of BB group was greater than other crossbreds at the age of 6 weeks (p<0.05). There was a significant difference in weekly body weight gains (p<0.05), which were 573, 991, 850, and 371 g at 2, 4, 6, and 8 weeks old, respectively. Uniformity of 4 crossbreds was 84.9%, 80.5%, and 72.5% at 6, 7, and 8 weeks, respectively, and there was no difference among crossbreds. Body weight gain of BB crossbred was highest among crossbreds (p<0.05). Weekly feed intake significantly increased with weeks as 669, 1,839, 2,812, and 3,381 g at 2, 4, 6, and 8 weeks respectively (p<0.05). Feed intakes of AA and BB crossbreds were higher at 2 to 4 weeks old than others and that of BB crossbred was highest at 4 to 6 weeks old (p<0.05). Weekly feed conversion ratios were 1.17, 1.86, 3.32, and 9.37 at 0 to 2, 2 to 4, 4 to 6, and 6 to 8 weeks old, respectively, and it increased with age (p<0.05). There was no significant difference in feed conversion ratio among crossbreds. Carcass yields of 4 crossbreds were 73.6%, 71.6%, 73.5%, and 71.7%, respectively, so there was no significant difference among crossbreds. There was no difference in wing, neck, breast and leg ratios among crossbreds. However, back ratios of 4 crossbreds were 17.6%, 18.0%, 15.8%, and 17.6%, respectively, and back ratio of BB was the highest among crossbreds. Finally, these results may provide the basic data on the production, carcass quality, fatty acid and amino acid composition of commercial KND with 2-way crossbreeding

Prediction of epigenetically regulated genes in breast cancer cell lines

Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology and progression, while revealing potentially new biomarkers. We have examined a recently developed high-throughput technology for measuring genome-wide methylation patterns called mTACL. Here, we propose a computational pipeline for integrating gene expression and CpG island methylation profles to identify epigenetically regulated genes for a panel of 45 breast cancer cell lines, which is widely used in the Integrative Cancer Biology Program (ICBP). The pipeline (i) reduces the dimensionality of the methylation data, (ii) associates the reduced methylation data with gene expression data, and (iii) ranks methylation-expression associations according to their epigenetic regulation. Dimensionality reduction is performed in two steps: (i) methylation sites are grouped across the genome to identify regions of interest, and (ii) methylation profles are clustered within each region. Associations between the clustered methylation and the gene expression data sets generate candidate matches within a fxed neighborhood around each gene. Finally, the methylation-expression associations are ranked through a logistic regression, and their significance is quantified through permutation analysis. Our two-step dimensionality reduction compressed 90% of the original data, reducing 137,688 methylation sites to 14,505 clusters. Methylation-expression associations produced 18,312 correspondences, which were used to further analyze epigenetic regulation. Logistic regression was used to identify 58 genes from these correspondences that showed a statistically signifcant negative correlation between methylation profles and gene expression in the panel of breast cancer cell lines. Subnetwork enrichment of these genes has identifed 35 common regulators with 6 or more predicted markers. In addition to identifying epigenetically regulated genes, we show evidence of differentially expressed methylation patterns between the basal and luminal subtypes. Our results indicate that the proposed computational protocol is a viable platform for identifying epigenetically regulated genes. Our protocol has generated a list of predictors including COL1A2, TOP2A, TFF1, and VAV3, genes whose key roles in epigenetic regulation is documented in the literature. Subnetwork enrichment of these predicted markers further suggests that epigenetic regulation of individual genes occurs in a coordinated fashion and through common regulators