Wound healing in rabbit corneas after flapless refractive lenticule extraction with a 345 nm ultraviolet femtosecond laser

Purpose To characterize corneal wound healing in a rabbit model after flapless refractive lenticule extraction with a 345 nm ultraviolet femtosecond laser. Setting Departments of Ophthalmology and Anatomy II, University of Erlangen-Nürnberg and Wavelight GmbH, Erlangen, Germany. Design Methods Flapless refractive lenticule extraction was performed in 1 eye each of 20 New Zealand white rabbits (−5.0 diopters). Groups of 4 animals were euthanized after 48 hours, 1 week, 2 weeks, 4 weeks, and 3 months, respectively. Corneal samples were prepared for histology and fluorescence microscopy. To assess corneal cell death, proliferation, and myofibroblastic transdifferentiation, terminal uridine deoxynucleotidyl nick end-labeling (TUNEL) assay as well as immunostaining for Ki67 and α-smooth muscle actin (αSMA) were performed on sagittal cryosections. Results Histology revealed a zone of keratocyte depletion with a thickness of approximately 50 μm around the extraction site. At 48 hours, pronounced TUNEL staining of keratocytes was detected around the interface (159.9 cells/mm ± 18.4 [SD]), which steadily decreased to 74.9 ± 19.8 cells/mm at 1 week and 5.7 ± 4.8 cells/mm at 2 weeks. Ki67 staining of keratocytes was evident at 48 hours (10.0 ± 3.8 cells/mm), which then decreased at 1 week (5.2 ± 1.7 cells/mm) and 2 weeks (0.4 ± 0.5 cells/mm). From 4 weeks onward, no TUNEL or Ki67 staining was detected. The corneal stroma was αSMA-negative at all timepoints. Conclusion Application of the 345 nm laser showed no signs of problematic repair processes in the cornea, which supports the initiation of the clinical phase

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

Diverse soil carbon dynamics expressed at the molecular level

The stability and potential vulnerability of soil organic matter (SOM) to global change remains incompletely understood due to the complex processes involved in its formation and turnover. Here we combine compound-specific radiocarbon analysis with fraction-specific and bulk-level radiocarbon measurements in order to further elucidate controls on SOM dynamics in a temperate and sub-alpine forested ecosystem. Radiocarbon contents of individual organic compounds isolated from the same soil interval generally exhibit greater variation than those among corresponding operationally-defined fractions. Notably, markedly older ages of long-chain plant leaf wax lipids (n-alkanoic acids) imply that they reflect a highly stable carbon pool. Furthermore, marked 14C variations among shorter- and longer-chain n-alkanoic acid homologues suggest that they track different SOM pools. Extremes in SOM dynamics thus manifest themselves within a single compound class. This exploratory study highlights the potential of compound-specific radiocarbon analysis for understanding SOM dynamics in ecosystems potentially vulnerable to global change

Simulations of the grand design galaxy M51: a case study for analysing tidally induced spiral structure

We present hydrodynamical models of the grand design spiral M51 (NGC 5194), and its interaction with its companion NGC 5195. Despite the simplicity of our models, our simulations capture the present day spiral structure of M51 remarkably well, and even reproduce details such as a kink along one spiral arm, and spiral arm bifurcations. We investigate the offset between the stellar and gaseous spiral arms, and find at most times (including the present day) there is no offset between the stars and gas to within our error bars. We also compare our simulations with recent observational analysis of M51. We compute the pattern speed versus radius, and like the observations, find no single global pattern speed. We also show that the spiral arms cannot be fitted well by logarithmic spirals. We interpret these findings as evidence that M51 does not exhibit a quasi-steady density wave, as would be predicted by density wave theory. The internal structure of M51 derives from the complicated and dynamical interaction with its companion, resulting in spiral arms showing considerable structure in the form of short-lived kinks and bifurcations. Rather than trying to model such galaxies in terms of global spiral modes with fixed pattern speeds, it is more realistic to start from a picture in which the spiral arms, while not being simple material arms, are the result of tidally induced kinematic density `waves' or density patterns, which wind up slowly over time.Comment: 23 pages, 20 figures, accepted for publication in MNRA

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

Microbially mediated reduction of FeIII and AsV in Cambodian sediments amended with 13C-labelled hexadecane and kerogen

Microbial activity is generally accepted to play a critical role, with the aid of suitable organic carbon substrates, in the mobilisation of arsenic from sediments into shallow reducing groundwaters. The nature of the organic matter in natural aquifers driving the reduction of AsV to AsIII is of particular importance but is poorly understood. In this study, sediments from an arsenic rich aquifer in Cambodia were amended with two 13C-labelled organic substrates. 13C-hexadecane was used as a model for potentially bioavailable long chain n-alkanes and a 13C-kerogen analogue as a proxy for non-extractable organic matter. During anaerobic incubation for 8 weeks, significant FeIII reduction and AsIII mobilisation were observed in the biotic microcosms only, suggesting that these processes were microbially driven. Microcosms amended with 13C-hexadecane exhibited a similar extent of FeIII reduction to the non-amended microcosms, but marginally higher AsIII release. Moreover, gas chromatography–mass spectrometry analysis showed that 65 % of the added 13C-hexadecane was degraded during the 8-week incubation. The degradation of 13C-hexadecane was microbially driven, as confirmed by DNA stable isotope probing (DNA-SIP). Amendment with 13C-kerogen did not enhance FeIII reduction or AsIII mobilisation, and microbial degradation of kerogen could not be confirmed conclusively by DNA-SIP fractionation or 13C incorporation in the phospholipid fatty acids. These data are, therefore, consistent with the utilisation of long chain n-alkanes (but not kerogen) as electron donors for anaerobic processes, potentially including FeIII and AsV reduction in the subsurface

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

Natural-abundance radiocarbon as a tracer of assimilation of petroleum carbon by bacteria in salt marsh sediments

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 70 (2006): 1761-1771, doi:10.1016/j.gca.2005.12.020.The natural abundance of radiocarbon (14C) provides unique insight into the source and cycling of sedimentary organic matter. Radiocarbon analysis of bacterial phospholipid lipid fatty acids (PLFAs) in salt-marsh sediments of southeast Georgia (USA) – one heavily contaminated by petroleum residues – was used to assess the fate of petroleum-derived carbon in sediments and incorporation of fossil carbon into microbial biomass. PLFAs that are common components of eubacterial cell membranes (e.g., branched C15 and C17, 10-methyl-C16) were depleted in 14C in the contaminated sediment (mean Δ14C value of +25 ± 19 ‰ for bacterial PLFAs) relative to PLFAs in uncontaminated “control” sediment (Δ14C = +101 ± 12‰). We suggest that the 14C-depletion in bacterial PLFAs at the contaminated site results from microbial metabolism of petroleum and subsequent incorporation of petroleum-derived carbon into bacterial membrane lipids. A mass balance calculation indicates that 6-10% of the carbon in bacterial PLFAs at the oiled site could derive from petroleum residues. These results demonstrate that even weathered petroleum may contain components of sufficient lability to be a carbon source for biomass production by marsh sediment microorganisms. Furthermore, a small but significant fraction of fossil carbon is assimilated even in the presence of a much larger pool of presumably more-labile and faster-cycling carbon substrates.This study was supported by Georgia Sea Grant (RR100-221/926784), the National Science Foundation (OCE-9911678) and NOSAMS (thanks to J. M. Hayes)

Compound-specific radiocarbon dating of the varved Holocene sedimentary record of Saanich Inlet, Canada

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 19 (2004): PA2012, doi:10.1029/2003PA000927.The radiocarbon contents of various biomarkers extracted from the varve-counted sediments of Saanich Inlet, Canada, were determined to assess their applicability for dating purposes. Calibrated ages obtained from the marine planktonic archaeal biomarker crenarchaeol compared favorably with varve-count ages. The same conclusion could be drawn for a more general archaeal biomarker (GDGT-0), although this biomarker proved to be less reliable due to its less-specific origin. The results also lend support to earlier indications that marine crenarchaeota use dissolved inorganic carbon (DIC) as their carbon source. The average reservoir age offset ΔR of 430 years, determined using the crenarchaeol radiocarbon ages, varied by ±110 years. This may be caused by natural variations in ocean-atmosphere mixing or upwelling at the NE Pacific coast but variability may also be due to an inconsistency in the marine calibration curve when used at sites with high reservoir ages.This work was supported by the Netherlands Organization for Scientific Research (NWO) and NSF grants OCE-9907129 and OCE-0137005 (Eglinton)

Direct application of compound-specific radiocarbon analysis of leaf waxes to establish lacustrine sediment chronology

Author Posting. © Springer, 2007. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Paleolimnology 39 (2008): 43-60, doi:10.1007/s10933-007-9094-1.This study demonstrates use of compound-specific radiocarbon analysis (CSRA) for dating Holocene lacustrine sediments from carbonate-hosted Ordy Pond, Oahu, Hawaii. Long-chain odd-numbered normal alkanes (n-alkanes), biomarkers characteristic of terrestrial higher plants, were ubiquitous in Ordy Pond sediments. The δ13C of individual n-alkanes ranged from −29.9 to −25.5‰, within the expected range for n-alkanes synthesized by land plants using the C3 or C4 carbon fixation pathway. The 14C ages of n-alkanes determined by CSRA showed remarkably good agreement with 14C dates of rare plant macrofossils obtained from nearby sedimentary horizons. In general, CSRA of n-alkanes successfully refined the age-control of the sediments. The sum of n-alkanes in each sample produced 70–170 μg of carbon (C), however, greater age errors were confirmed for samples containing less than 80 μg of C. The 14C age of n-alkanes from one particular sedimentary horizon was 4,155 years older than the value expected from the refined age-control, resulting in an apparent and arguable age discrepancy. Several lines of evidence suggest that this particular sample was contaminated by introduction of 14C-free C during preparative capillary gas chromatography. This study simultaneously highlighted the promising potential of CSRA for paleo-applications and the risks of contamination associated with micro-scale 14C measurement of individual organic compounds.This project was funded by Petroleum Research Fund (PRF #40088-ACS) and in part by Sigma Xi, The Scientific Research Society (Grants in aid of research, 2003)