Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation

Background Metatranscriptome sequence data can contain highly redundant sequences from diverse populations of microbes and so data reduction techniques are often applied before taxonomic and functional annotation. For metagenomic data, it has been observed that the variable coverage and presence of closely related organisms can lead to fragmented assemblies containing chimeric contigs that may reduce the accuracy of downstream analyses and some advocate the use of alternate data reduction techniques. However, it is unclear how such data reduction techniques impact the annotation of metatranscriptome data and thus affect the interpretation of the results. Results To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. For the Illumina simulations, we found that a two-step approach of assembly followed by clustering of contigs and unassembled sequences produced the most accurate reflection of the real protein domain content of the sample. For the 454 simulations, the combined annotation of contigs and unassembled reads produced the most accurate protein domain annotations. Conclusions Based on these data we recommend that assembly be attempted, and that unassembled reads be included in the final annotation for metatranscriptome data, even from highly diverse environments as the resulting annotations should lead to a more accurate reflection of the transcriptional behaviour of the microbial population under investigation

Global discovery and characterization of small non-coding RNAs in marine microalgae

Background Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions

Framework for the Analysis of the Adaptability, Extensibility, and Scalability of Semantic Information Integration and the Context Mediation Approach

Technological advances such as Service Oriented Architecture (SOA) have increased the feasibility and importance of effectively integrating information from an ever widening number of systems within and across enterprises. A key difficulty of achieving this goal comes from the pervasive heterogeneity in all levels of information systems. A robust solution to this problem needs to be adaptable, extensible, and scalable. In this paper, we identify the deficiencies of traditional semantic integration approaches. The COntext INterchange (COIN) approach overcomes these deficiencies by declaratively representing data semantics and using a mediator to create the necessary conversion programs from a small number of conversion rules. The capabilities of COIN is demonstrated using an example with 150 data sources, where COIN can automatically generate the over 22,000 conversion programs needed to enable semantic interoperability using only six parametizable conversion rules. This paper presents a framework for evaluating adaptability, extensibility, and scalability of semantic integration approaches. The application of the framework is demonstrated with a systematic evaluation of COIN and other commonly practiced approaches.This work has been supported, in part, by MITRE Corp., the MIT-MUST project, the Singapore-MIT Alliance, and Suruga Bank

Semantic Information Integration in the Large: Adaptability, Extensibility, and Scalability of the Context Mediation Approach

There is pressing need for effectively integrating information from an ever increasing number of available sources both on the web and in other existing systems. A key difficulty of achieving this goal comes from the pervasive heterogeneities in all levels of information systems. Existing and emerging technologies, such as the Web, ODBC, XML, and Web Services, provide essential capabilities in resolving heterogeneities in the hardware and software platforms, but they do not address the semantic heterogeneity of the data itself. A robust solution to this problem needs to be adaptable, extensible, and scalable. In this paper, we identify the deficiencies of traditional approaches that address this problem using hand-coded programs or require complete data standardization. The COntext INterchange (COIN) approach overcomes these deficiencies by declaratively representing data semantics and using a mediator to create the necessary conversion programs using a small number of conversion rules. The capabilities of COIN is demonstrated using an intelligence information integration example consisting of 150 data sources, where COIN can automatically generate the over 22,000 conversion programs needed to enable semantic integration using only six parametizable conversion rules. This paper makes a unique contribution by providing a systematic evaluation of COIN and other commonly practiced approaches

Residents' reactions to long-term sonic boom exposure: Preliminary results

This presentation is about residents' reactions to sonic booms in a long-term sonic boom exposure environment. Although two phases of the data collection have been completed, the analysis of the data has only begun. The results are thus preliminary. The list of four authors reflects the complex multi-disciplinary character of any field study such as this one. Carey Moulton is responsible for Wyle Laboratories' acoustical data collection effort. Robert Baumgartner and Jeff Thomas of HBRS, a social science research firm, are responsible for social survey field work and data processing. The study is supported by the NASA Langley Research Center. The study has several objectives. The preliminary data addresses two of the primary objectives. The first objective is to describe the reactions to sonic booms of people who are living where sonic booms are a routine, recurring feature of the acoustical environment. The second objective is to compare these residents' reactions to the reactions of residents who hear conventional aircraft noise around airports. Here is an overview of the presentation. This study will first be placed in the context of previous community survey research on sonic booms. Next the noise measurement program will be briefly described and part of a social survey interview will be presented. Finally data will be presented on the residents' reactions and these reactions will be compared with reactions to conventional aircraft. Twelve community studies of residents' reactions to sonic booms were conducted in the United States and Europe in the 1960's and early 1970's. None of the 12 studies combined three essential ingredients that are found in the present study. Residents' long-term responses are related to a measured noise environment. Sonic booms are a permanent feature of the residential environment. The respondents' do not live on a military base. The present study is important because it provides the first dose/response relationship for sonic booms that could be expected to apply to residents in civilian residential areas

Genetic Variation in North American Black Flies in the Subgenus \u3ci\u3ePsilopelmia\u3c/i\u3e (\u3ci\u3eSimulium\u3c/i\u3e: Diptera: Simuliidae)

Resolution of the genetic heterogeneity of closely related insect species depends on the selection of reliable genetic markers derived from representative specimens. We report the results of a survey of genetic variability in nine species of black flies in the subgenus Psilopelmia Enderlein. Three regions of the mitochondrial genome and an amplicon including the internal transcribed spacer 1 of the nuclear ribosomal RNA gene cluster (ITS1) were amplified using the polymerase chain reaction (PCR), and the amplicons were examined for intraspecific and interspecific polymorphisms. Six of the seven Psilopelmia species that yielded PCR products in the ITS1 PCR reaction were found to generate products that were indistinguishable on the basis of size. Similarly, little interspecific variation was noted in the 16S rRNA amplicon among nine species of Psilopelmia assayed by heteroduplex analysis. In contrast, the remaining regions of the mitochondrial genome exhibited both intra- and inter-specific variation when analyzed by heteroduplex analysis. Information collected from the five amplicons could be employed to develop a classification scheme capable of distinguishing the nine species of Psilopelmia examined

Semantic Information Integration in the Large: Adaptability, Extensibility, and Scalability of the Context Mediation Approach

There is pressing need for effectively integrating information from an ever increasing number of available sources both on the web and in other existing systems. A key difficulty of achieving this goal comes from the pervasive heterogeneities in all levels of information systems. Existing and emerging technologies, such as the Web, ODBC, XML, and Web Services, provide essential capabilities in resolving heterogeneities in the hardware and software platforms, but they do not address the semantic heterogeneity of the data itself. A robust solution to this problem needs to be adaptable, extensible, and scalable. In this paper, we identify the deficiencies of traditional approaches that address this problem using hand-coded programs or require complete data standardization. The COntext INterchange (COIN) approach overcomes these deficiencies by declaratively representing data semantics and using a mediator to create the necessary conversion programs using a small number of conversion rules. The capabilities of COIN is demonstrated using an intelligence information integration example consisting of 150 data sources, where COIN can automatically generate the over 22,000 conversion programs needed to enable semantic integration using only six parametizable conversion rules. This paper makes a unique contribution by providing a systematic evaluation of COIN and other commonly practiced approaches

Invertebrate metrics based on few abundant taxa outperform functional and taxonomic composition as indicators of agricultural impacts in Atlantic rainforest streams

Metacommunity studies have demonstrated that local macroinvertebrate communities are structured not only by local environmental conditions but also by spatial processes. Effective bioassessment tools should account for spatial processes while doing so with the least amount of cost. In this study, we applied variance partition techniques based on redundancy analysis to assess the performance of three sets of benthic invertebrate metrics in detecting agricultural land-use effects in a SE Brazil rainforest watershed. Macroinvertebrate data were analyzed separately regarding their taxonomic, functional structure and bioindicator metrics developed for the study region. We stipulated that groups of metrics most sensitive to land-use effects should have the highest amount of variance explained by the joint effects of land use and environmental variation, independently of spatial structuring. Statistical analyses were repeated removing rare taxa in order to assess the effects of their inclusion in the responsiveness of each group of metrics. Traditional bioindicator metrics were more responsive to environmental variation associated with agriculture than taxa abundances and functional attributes. Furthermore, a few common taxa drove a high proportion of the variation observed in invertebrate communities, regardless of how invertebrate data were organized. Similar analytic approaches have the potential to be useful in curtailing sorting and identification efforts when developing macroinvertebrate-based biomonitoring protocols, especially in areas where information regarding the taxonomy of benthic communities is still poorly described

The origin of green icebergs in Antarctica

A comparison of samples from a translucent green iceberg with a core from the Ronne Ice Shelf revealed an excellent agreement in isotopic composition, crystal structure, and incorporated sediment particles. Marine shelf ice which constitutes the basal portion of some ice shelves is considered to be the source of green icebergs. It most likely results from "ice pump" processes which produce large amounts of ice platelets in the water column beneath ice shelves. These subsequently accumulate and become compacted into bubble-free, desalinated ice. Iceberg and drift-buoy trajectories indicate that green icebergs observed in the Weddell Sea originate from the Amery Ice Shelf rather than from the Ronne Ice Shelf, although the latter ice shelf is also a potential source