Macroinvertebrate community responses to a dewatering disturbance gradient in a restored stream

Dewatering disturbances are common in aquatic systems and represent a relatively untapped field of disturbance ecology, yet studying dewatering events along gradients in non-dichotomous (i.e. wet/dry) terms is often difficult. Because many stream restorations can essentially be perceived as planned hydrologic manipulations, such systems can make ideal test-cases for understanding processes of hydrological disturbance. In this study we used an experimental drawdown in a 440 ha stream/wetland restoration site to assess aquatic macroinvertebrate community responses to dewatering and subsequent rewetting. The geomorphic nature of the site and the design of the restoration allowed dewatering to occur predictably along a gradient and decoupled the hydrologic response from any geomorphic (i.e. habitat heterogeneity) effects. In the absence of such heterogeneous habitat refugia, reach-scale wetted perimeter and depth conditions exerted a strong control on community structure. The community exhibited an incremental response to dewatering severity over the course of this disturbance, which was made manifest not as a change in community means but as an increase in community variability, or dispersion, at each site. The dewatering also affected inter-species abundance and distributional patterns, as dewatering and rewetting promoted alternate species groups with divergent habitat tolerances. Finally, our results indicate that rapid rewetting – analogous to a hurricane breaking a summer drought – may represent a recovery process rather than an additional disturbance and that such processes, even in newly restored systems, may be rapid

Technical and Economic Assessment of Span-Distributed Loading Cargo Aircraft Concepts

A 700,000 kg (1,540,000-lb) aircraft with a cruise Mach number of 0.75 was found to be optimum for the specified mission parameters of a 272 155-kg (600,000-lb) payload, a 5560-km (3000-n.mi.) range, and an annual productivity of 113 billion revenue-ton km (67 billion revenue-ton n. mi.). The optimum 1990 technology level spanloader aircraft exhibited the minimum 15-year life-cycle costs, direct operating costs, and fuel consumption of all candidate versions. Parametric variations of wing sweep angle, thickness ratio, rows of cargo, and cargo density were investigated. The optimum aircraft had two parallel rows of 2.44 x 2.44-m (8 x 8-ft) containerized cargo with a density of 160 kg/cu m (10 lb/ft 3) carried throughout the entire 101-m (331-ft) span of the constant chord, 22-percent thick, supercritical wing. Additional containers or outsized equipment were carried in the 24.4-m (80-ft) long fuselage compartment preceding the wing. Six 284,000-N (64,000-lb) thrust engines were mounted beneath the 0.7-rad (40-deg) swept wing. Flight control was provided by a 36.6-m (120-ft) span canard surface mounted atop the forward fuselage, by rudders on the wingtip verticals and by outboard wing flaperons

Genetic control of maize shoot apical meristem architecture

The shoot apical meristem contains a pool of undifferentiated stem cells and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 · Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (629 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, whereas those for unrelated traits did not overlap. With the use of three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions. © 2014 Thompson et al

Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

Transcriptome variation plays an important role in affecting the phenotype of an organism. However, an understanding of the underlying mechanisms regulating transcriptome variation in segregating populations is still largely unknown. We sought to assess and map variation in transcript abundance in maize shoot apices in the intermated B73×Mo17 recombinant inbred line population. RNA-based sequencing (RNA-seq) allowed for the detection and quantification of the transcript abundance derived from 28,603 genes. For a majority of these genes, the population mean, coefficient of variation, and segregation patterns could be predicted by the parental expression levels. Expression quantitative trait loci (eQTL) mapping identified 30,774 eQTL including 96 trans-eQTL "hotspots," each of which regulates the expression of a large number of genes. Interestingly, genes regulated by a trans-eQTL hotspot tend to be enriched for a specific function or act in the same genetic pathway. Also, genomic structural variation appeared to contribute to cis-regulation of gene expression. Besides genes showing Mendelian inheritance in the RIL population, we also found genes whose expression level and variation in the progeny could not be predicted based on parental difference, indicating that non-Mendelian factors also contribute to expression variation. Specifically, we found 145 genes that show patterns of expression reminiscent of paramutation such that all the progeny had expression levels similar to one of the two parents. Furthermore, we identified another 210 genes that exhibited unexpected patterns of transcript presence/absence. Many of these genes are likely to be gene fragments resulting from transposition, and the presence/absence of their transcripts could influence expression levels of their ancestral syntenic genes. Overall, our results contribute to the identification of novel expression patterns and broaden the understanding of transcriptional variation in plants. © 2013 Lin et al

Genic and nongenic contributions to natural variation of quantitative traits in maize

The complex genomes of many economically important crops present tremendous challenges to understand the genetic control of many quantitative traits with great importance in crop production, adaptation, and evolution. Advances in genomic technology need to be integrated with strategic genetic design and novel perspectives to break new ground. Complementary to individual-gene-targeted research, which remains challenging, a global assessment of the genomic distribution of trait-associated SNPs (TASs) discovered from genome scans of quantitative traits can provide insights into the genetic architecture and contribute to the design of future studies. Here we report the first systematic tabulation of the relative contribution of different genomic regions to quantitative trait variation in maize. We found that TASs were enriched in the nongenic regions, particularly within a 5-kb window upstream of genes, which highlights the importance of polymorphisms regulating gene expression in shaping the natural variation. Consistent with these findings, TASs collectively explained 44%-59% of the total phenotypic variation across maize quantitative traits, and on average, 79% of the explained variation could be attributed to TASs located in genes or within 5 kb upstream of genes, which together comprise only 13% of the genome. Our findings suggest that efficient, cost-effective genome-wide association studies (GWAS) in species with complex genomes can focus on genic and promoter regions

Genome-wide discovery and characterization of maize long non-coding RNAs

BACKGROUND: Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. RESULTS: By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans- genetic factors. CONCLUSIONS: We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5\u27 ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ~100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 X 10-5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny

A Precision Measurement of Nuclear Muon Capture on 3He

The muon capture rate in the reaction mu- 3He -> nu + 3H has been measured at PSI using a modular high pressure ionization chamber. The rate corresponding to statistical hyperfine population of the mu-3He atom is (1496.0 +- 4.0) s^-1. This result confirms the PCAC prediction for the pseudoscalar form factors of the 3He-3H system and the nucleon.Comment: 13 pages, 6 PostScript figure

Trastuzumab-associated cardiac adverse effects in the Herceptin adjuvant trial.

PURPOSE: The purpose of this analysis was to investigate trastuzumab-associated cardiac adverse effects in breast cancer patients after completion of (neo)adjuvant chemotherapy with or without radiotherapy. PATIENTS AND METHODS: The Herceptin Adjuvant (HERA) trial is a three-group, multicenter, open-label randomized trial that compared 1 or 2 years of trastuzumab given once every 3 weeks with observation in patients with HER-2-positive breast cancer. Only patients who after completion of (neo)adjuvant chemotherapy with or without radiotherapy had normal left ventricular ejection fraction (LVEF > or = 55%) were eligible. A repeat LVEF assessment was performed in case of cardiac dysfunction. RESULTS: Data were available for 1,693 patients randomly assigned to 1 year trastuzumab and 1,693 patients randomly assigned to observation. The incidence of trastuzumab discontinuation due to cardiac disorders was low (4.3%). The incidence of cardiac end points was higher in the trastuzumab group compared with observation (severe congestive heart failure [CHF], 0.60% v 0.00%; symptomatic CHF, 2.15% v 0.12%; confirmed significant LVEF drops, 3.04% v 0.53%). Most patients with cardiac dysfunction recovered in fewer than 6 months. Patients with trastuzumab-associated cardiac dysfunction were treated with higher cumulative doses of doxorubicin (287 mg/m(2) v 257 mg/m(2)) or epirubicin (480 mg/m(2) v 422 mg/m(2)) and had a lower screening LVEF and a higher body mass index. CONCLUSION: Given the clear benefit in disease-free survival, the low incidence of cardiac adverse events, and the suggestion that cardiac dysfunction might be reversible, adjuvant trastuzumab should be considered for treatment of breast cancer patients who fulfill the HERA trial eligibility criteri

Positional cloning of the barley tillering gene uniculme4

Manipulation of plant architectural traits such as the number of tillers can effectively increase grain yield in cereals. Within the frame of the TriticeaeGenome project (www.triticeaegenome.eu), the objective of our group was the fine mapping and positional cloning of uniculme4 (cul4), a gene required for tillering in barley. Based on initial medium resolution mapping of the locus, a segregating population including 4900 F3 plants was developed and genotyped with three tightly linked SNP markers (Tavakol et al., abstract P321, PAG XIX). The locus was further resolved through mapping of 8 synteny-derived markers allowing the identification of a candidate gene that co-segregates with the cul4 phenotype. The two genes that flank the candidate gene in Brachypodium and rice were positioned 0.11 cM and 0.12 cM from cul4, respectively: development of new markers is underway using sequence information from two BACs anchored to the physical map and spanning this region. The intron-exon structure of the candidate gene was determined from a cDNA isolated from wild-type plants. Resequencing of independent cul4 stocks identified three distinct mutations within the candidate gene, including a deletion of the 5\u2019 region. Comparison of expression levels and patterns in mutant and wild-type plants is underway