Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity

Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing

Abstract Background Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21-24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. Results We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analysed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. Conclusion We have discovered and analysed a large number of conserved and melon-specific sRNAs, including miRNAs and their potential target genes. This provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melon-virus interactions.This work was supported by grants AGL2009-07552/AGR, BIO2006-13107 (Ministerio de Ciencia e Innovación, Spain) and MELONOMICS (Fundación Genoma España, Spain).Peer Reviewe

The Advancement of Public Awareness, Concerning TRU Waste Characterization, Using a Virtual Document

Building public trust and confidence through openness is a goal of the DOE Carlsbad Field Office for the Waste Isolation Pilot Plant (WIPP). The objective of the virtual document described in this paper is to give the public an overview of the waste characterization steps, an understanding of how waste characterization instrumentation works, and the type and amount of data generated from a batch of drums. The document is intended to be published on a web page and/or distributed at public meetings on CDs. Users may gain as much information as they desire regarding the transuranic (TRU) waste characterization program, starting at the highest level requirements (drivers) and progressing to more and more detail regarding how the requirements are met. Included are links to: drivers (which include laws, permits and DOE Orders); various characterization steps required for transportation and disposal under WIPP's Hazardous Waste Facility Permit; physical/chemical basis for each characterization method; types of data produced; and quality assurance process that accompanies each measurement. Examples of each type of characterization method in use across the DOE complex are included. The original skeleton of the document was constructed in a PowerPoint presentation and included descriptions of each section of the waste characterization program. This original document had a brief overview of Acceptable Knowledge, Non-Destructive Examination, Non-Destructive Assay, Small Quantity sites, and the National Certification Team. A student intern was assigned the project of converting the document to a virtual format and to discuss each subject in depth. The resulting product is a fully functional virtual document that works in a web browser and functions like a web page. All documents that were referenced, linked to, or associated, are included on the virtual document's CD. WIPP has been engaged in a variety of Hazardous Waste Facility Permit modification activities. During the public meetings, discussion centered on proposed changes to the characterization program. The philosophy behind the virtual document is to show the characterization process as a whole, rather than as isolated parts. In addition to public meetings, other uses for the information might be as a training tool for new employees at the WIPP facility to show them where their activities fit into the overall scheme, as well as an employee review to help prepare for waste certification audits

Predicting landscape‐level distribution and abundance: Integrating demography, fire, elevation and landscape habitat configuration

Demography varies in response to multiple interactive drivers at varying scales. However, these relationships are often assessed piecemeal, particularly without consideration of drivers at the landscape level. We developed a model to predict population dynamics of an endangered, perennial herb Hypericum cumulicola across a range of landscape drivers. We estimated vital rates using 22 years of annual census data from 15 populations (10,910 and 38,313 unique observations) and additional seeding experiments, considering four landscape drivers (time-since-fire, patch area, patch aggregation and patch elevation). We combined these models into integral projection models to assess population parameters. Predictions of occupancy and density were compared with an independent dataset of 33 habitat patches. We also evaluated the effect of fire-return interval on population persistence. The landscape drivers had interactive effects on vital rates and demography. Occupancy was predicted for most patches, including many that were unoccupied. Abundances were poorly predicted, primarily because projections were unreliable for patches having intermediate areas and aggregation. When these patches were removed, the model explained 42% of the variance in abundance. Projected population growth was greater and extinction risk lower under more frequent fire-return intervals, at higher elevations, and in larger and more aggregated patches. Our modelling suggests that fire can be prescribed less often in larger than smaller patches to support a viable metapopulation of H. cumulicola. Synthesis. The integration of landscape-level drivers and detailed demographic data is a valuable tool for understanding species abundances, distributions and dynamics at large scales. We evaluated the effect of interactions among fire, patch elevation, area and aggregation on the demography of a rare and endangered plant. Our findings reinforce the importance of regional dynamics. These drivers and their interactions suggest locations that can support higher vital rates, occupancy and abundance, and what fire-return intervals are optimal depending on landscape characteristics. This approach demonstrates a link between plant demography and landscape variables, although further work is needed to improve ecological predictions

Modeling source-filter interaction in belting and high-pitched operatic male singing

Nonlinear source-filter theory is applied to explain some acoustic differences between two contrasting male singing productions at high pitches: operatic style versus jazz belt or theater belt. Several stylized vocal tract shapes (caricatures) are discussed that form the bases of these styles. It is hypothesized that operatic singing uses vowels that are modified toward an inverted megaphone mouth shape for transitioning into the high-pitch range. This allows all the harmonics except the fundamental to be “lifted” over the first formant. Belting, on the other hand, uses vowels that are consistently modified toward the megaphone (trumpet-like) mouth shape. Both the fundamental and the second harmonic are then kept below the first formant. The vocal tract shapes provide collective reinforcement to multiple harmonics in the form of inertive supraglottal reactance and compliant subglottal reactance. Examples of lip openings from four well-known artists are used to infer vocal tract area functions and the corresponding reactances