Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

<p>Abstract</p> <p>Background</p> <p>The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels.</p> <p>Results</p> <p>Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F₂mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F₂populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F₂, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 <it>D. carota </it>accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity.</p> <p>Conclusions</p> <p>The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.</p

Performance of Supply Chain when using selected Coordination Mechanisms

Coordination among supply chain members is essential for better supply chain performance. An effective method to improve supply chain coordination is to implement proper coordination mechanisms. The primary objective of this research is to study the performance of a multi-level supply chain while using selected coordination mechanisms separately, and in combination, under lost sale and back order cases. The coordination mechanisms used in this study are price discount, delay in payment and different types of information sharing. Mathematical modelling and simulation modelling are used in this study to analyse the performance of the supply chain using these mechanisms. Initially, a three level supply chain consisting of a supplier, a manufacturer and a retailer has been used to study the combined effect of price discount and delay in payment on the performance (profit) of supply chain using mathematical modelling. This study showed that implementation of individual mechanisms improves the performance of the supply chain compared to ‘no coordination’. When more than one mechanism is used in combination, performance in most cases further improved. The three level supply chain considered in mathematical modelling was then extended to a three level network supply chain consisting of a four retailers, two wholesalers, and a manufacturer with an infinite part supplier. The performance of this network supply chain was analysed under both lost sale and backorder cases using simulation modelling with the same mechanisms: ‘price discount and delay in payment’ used in mathematical modelling. This study also showed that the performance of the supply chain is significantly improved while using combination of mechanisms as obtained earlier. In this study, it is found that the effect (increase in profit) of ‘delay in payment’ and combination of ‘price discount’ & ‘delay in payment’ on SC profit is relatively high in the case of lost sale. Sensitivity analysis showed that order cost of the retailer plays a major role in the performance of the supply chain as it decides the order quantity of the other players in the supply chain in this study. Sensitivity analysis also showed that there is a proportional change in supply chain profit with change in rate of return of any player. In the case of price discount, elasticity of demand is an important factor to improve the performance of the supply chain. It is also found that the change in permissible delay in payment given by the seller to the buyer affects the SC profit more than the delay in payment availed by the buyer from the seller. In continuation of the above, a study on the performance of a four level supply chain consisting of a manufacturer, a wholesaler, a distributor and a retailer with ‘information sharing’ as coordination mechanism, under lost sale and backorder cases, using a simulation game with live players has been conducted. In this study, best performance is obtained in the case of sharing ‘demand and supply chain performance’ compared to other seven types of information sharing including traditional method. This study also revealed that effect of information sharing on supply chain performance is relatively high in the case of lost sale than backorder. The in depth analysis in this part of the study showed that lack of information sharing need not always be resulting in bullwhip effect. Instead of bullwhip effect, lack of information sharing produced a huge hike in lost sales cost or backorder cost in this study which is also not favorable for the supply chain. Overall analysis provided the extent of improvement in supply chain performance under different cases. Sensitivity analysis revealed useful insights about the decision variables of supply chain and it will be useful for the supply chain management practitioners to take appropriate decisions.Cochin University of Science & Technolog

Unusual case of immunoglobulin G4-related disease

Immunoglobulin G4-related disease is a group of disorders, which was thought to be unrelated at first and now grouped together due to their common characteristics. This case is being reported for its unique presentation, rarity, difficulty in diagnosis, and recognition of the existence of the disease entity in this part of the world

Modeling and parametric optimization of friction stir welding of aluminium alloy AA7068-T6 using response surface methodology and desirability function analysis

In this investigation, high specific strength precipitation hardenable alloy AA7068-T6 was joined using friction stir welding. Experiments were carried out using the three factor-three level central composite face-centered design of response surface methodology. Regression models were developed to assess the influence of tool rotational speed, welding speed, and axial force on ultimate tensile strength and elongation of the fabricated joints. The validity of the developed models was tested using the analysis of variance (ANOVA), actual and adjusted values of the regression coefficients, and experimental trials. The analysis of the developed models together with microstructural studies of typical cases showed that the tool rotational speed and welding speed have a significant interaction effect on the tensile strength and elongation of the joints. However, the axial force has a relatively low interaction effect with tool rotational speed and welding speed on the strength and elongation of the joints. The process variables were optimized using the desirability function analysis. The optimized values of joint tensile strength and elongation – 516 MPa and 21.57%, respectively were obtained at a tool rotational speed of 1218 rpm, welding speed of 47 mm/ min, and an axial force of 5.3 kN

Verification of treatment planning algorithms using optically stimulated luminescent dosimeters in a breast phantom

Aim: The aim of this study is to measure and compare the surface dose of treated breast and contralateral breast with the treatment planning system (TPS) calculated dose using calibrated optically stimulated luminescent dosimeter (OSLD) in an indigenous wax breast phantom. Materials and Methods: Three-dimensional conformal plans were generated in eclipse TPS v. 13 to treat the left breast of a wax phantom for a prescribed dose of 200 cGy. The plans were calculated using anisotropic analytical algorithm (AAA) and Acuros algorithm with 1-mm grid size. Calibrated OSLDs were used to measure the surface dose of treated and contralateral breasts. Results: Large differences were observed between measured and expected doses when OSLDs were read in “reading mode” compared to the “hardware mode.” The consistency in the responses of OSLDs was better (deviation <±5%) in the “hardware mode.” Reasonable agreement between TPS dose and measured dose was found in regions inside the treatment field of treated breast using OSLDs for both algorithms. OSLD measured doses and TPS doses, for the points where the angle of incidence was almost normal, were in good agreement compared to all other locations where the angle of incidence varied from 45° to 70°. The maximum deviation between measured doses and calculated doses with AAA and with Acuros were 2.2% and-12.38%, respectively, for planning target volume breast, and 76% and 77.51%, respectively, for the opposite breast. Conclusion: An independent calibration factor is required before using the OSLDs for in vivo dose measurements. With reference to measured doses using OSLD, the accuracy of skin dose estimation of TPS with AAA was better than with Acuros for both the breasts. In general, a reasonable agreement between TPS doses calculated using AAA and measured doses exists in regions inside treatment field, but unacceptable differences were observed for the points lateral to the opposite breast for both AAA and Acuros

Design and development of an inflatable latex balloon to reduce rectal and bladder doses for patients undergoing high dose rate brachytherapy

Multiple fractions of High Dose Rate (HDR) brachytherapy along with external beam therapy is the common method of treatment for cancer of the uterine cervix. Urinary bladder and rectum are the organs at risk (OARs) that receive a significant dose during treatment. To reduce the dose to these organs, a majority of hospitals use vaginal gauze packing, as it is a simple, nontraumatic, and easy method. This article describes the design and development of an inflatable balloon that can be used along with the applicator as a substitute for gauze packing. The balloon has two parts-the bladder part (B-part) and the rectum part (R-part), both of them are independently inflatable. The selection of the material, its width, length, and thickness are described. A mould/former for making the balloon was designed. Polished steel was used as the mould. This was dipped in specially prepared natural rubber latex (NRL) solution several times; the layers were dried and stripped to get the balloon. The composition of NRL and the compounding recipe of the latex are also described. Physical tests like tensile strength, elongation at break, bursting volume, and radiation attenuation caused by the balloon, were checked. Biological tests for assessing type I and type IV allergies, like dermal irritation and skin irritation tests, were also done