An endogenous small interfering RNA pathway in Drosophila

Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of 22 nucleotides in length, which arise from structured precursors through the action of Drosha - Pasha and Dicer- 1-Loquacious complexes(1-7). These join Argonaute-1 to regulate gene expression(8,9). A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons(10,11). Piwi- interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi- catalysed cleavage of single-stranded RNAs12,13. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer- 2, but a subset depends preferentially on Loquacious(1,4,5) rather than the canonical Dicer- 2 partner, R2D2 ( ref. 14). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue- specific fashion. They predominantly join Argonaute- 2 and have the capacity, as a class, to target both protein- coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles

Novel analytical techniques for improved decision making Implications for consumers and institutions

Information availability plays a key role in determining the choices of consumers, firms and governments.However, externalities associated with most commodities represent information failure leading toincorrect decisions. The emerging scientific advances nevertheless have produced several new analyticaltechniques that could guide towards better decisions. The objective of the paper is to review theexisting Iiterature on such analytical techniques and assess the appl icabi lity of such tools within the SriLankan context.Literature in environmental management and economics related disciplines revealed that availabilityof techniques such as Life cycle assessment (LCA) and food mile analysis for consumer productswhile institution or firm level decision making could be guided by tools such as management costaccounting and sustainable chain managementLCA has often been used in evaluating environmental performances of different food production andfood packaging options, waste management and transport options. The information of such analyseshas been made available through product standards such as ISO 14040. Food mile is an indicator oftransport costs offood items which could provide important guidelines for transport policy, internationaltrade and product related environmental information for consumeThe review elaborates on range of examples of application of such techniques over a wide range ofconsumer goods and services, institutions. The review reveals that although there seem to be sufficientanalytical techniques available worldwide, the applicability of such tools within Sri Lanka has beenvery sparse. LCA studies are only limited to two products and the ISO standards have not beenattempted yet. The study also highlights the need to improve the relevant data bases which wouldenable the rapid application of these tools and guide the decision maker towards sustainable directions.

Cost benefit analysis of village tank rehabilitation programme in Hambantota district, Sri Lanka

Village tanks provide multiple benefits to the local people living in their periphery and also to communitiesoutside the area. Non recognition of the true values of this resource has led to their degradation. Forexample, tank rehabilitation is usually not economically justifiable when the paddy benefits alone areconsidered. The main objective of this research was therefore to compare costs of village tankrehabilitation programme with the multiple benefits of village tanks.Villagers use tank water for agriculture, fish, domestic purposes, livestock rearing, and also for industrysuch as brick production. There are in addition, recreational benefits enjoyed by the households. Suchmultiple benefits have been evaluated by a survey conducted in 10 village tanks (7 isolated and 3cascade tanks) in Hambantota district of Sri Lanka. 175 households who live adjacent to the selectedtanks were interviewed using a pre-tested questionnaire with embedded contingent valuation surveyduring the maha season of2005/2006. Information on the use of tank system for purposes other thanpaddy cultivation was collected and contingent valuation method, market price approach and opportunitycost method were used in order to derive the economic value.The benefits and costs were analyzed in a cost benefit framework using a 20 year time period and10% discount rate. Results indicate that the rehabilitation project is only justifiable when multiplebenefits are included. When paddy benefits alone are compared with tank rehabilitation costs, itresults in negative net present value.The implications of the results in reversing the attitudes of the government towards small tanks andtheir role in enhancing rural economies are also discussed.

The Physics of the B Factories

This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C

Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline

Silencing of genomic repeats, including transposable elements, in Drosophila melanogaster is mediated by repeat-associated short interfering RNAs (rasiRNAs) interacting with proteins of the Piwi subfamily. rasiRNA-based silencing is thought to be mechanistically distinct from both the RNA interference and microRNA pathways. We show that the amount of rasiRNAs of a wide range of retroelements is drastically reduced in ovaries and testes of flies carrying a mutation in the spn-E gene. To address the mechanism of rasiRNA-dependent silencing of retrotransposons, we monitored their chromatin state in ovaries and somatic tissues. This revealed that the spn-E mutation causes chromatin opening of retroelements in ovaries, resulting in an increase in histone H3 K4 dimethylation and a decrease in histone H3 K9 di/trimethylation. The strongest chromatin changes have been detected for telomeric HeT-A elements that correlates with the most dramatic increase of their transcript level, compared to other mobile elements. The spn-E mutation also causes depletion of HP1 content in the chromatin of transposable elements, especially along HeT-A arrays. We also show that mutations in the genes controlling the rasiRNA pathway cause no derepression of the same retrotransposons in somatic tissues. Our results provide evidence that germinal Piwi-associated short RNAs induce chromatin modifications of their targets

Correlation of LNCR rasiRNAs Expression with Heterochromatin Formation during Development of the Holocentric Insect Spodoptera frugiperda

Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism