High dissimilarity within a multiyear annual record of pollen assemblages from a North American tallgrass prairie

Citation: Commerford, J. L., McLauchlan, K. K., & Minckley, T. A. (2016). High dissimilarity within a multiyear annual record of pollen assemblages from a North American tallgrass prairie. Ecology and Evolution, 6(15), 5273-5289. doi:10.1002/ece3.2259Grassland vegetation varies in composition across North America and has been historically influenced by multiple biotic and abiotic drivers, including fire, herbivory, and topography. Yet, the amount of temporal and spatial variability exhibited among grassland pollen assemblages, and the influence of these biotic and abiotic drivers on pollen assemblage composition and diversity has been relatively understudied. Here, we examine 4 years of modern pollen assemblages collected from a series of 28 traps at the Konza Prairie Long-Term Ecological Research Area in the Flint Hills of Kansas, with the aim of evaluating the influence of these drivers, as well as quantifying the amount of spatial and temporal variability in the pollen signatures of the tallgrass prairie biome. We include all terrestrial pollen taxa in our analyses while calculating four summative metrics of pollen diversity and composition -beta-diversity, Shannon index, nonarboreal pollen percentage, and Ambrosia: Artemisia -and find different roles of fire, herbivory, and topography variables in relation to these pollen metrics. In addition, we find significant annual differences in the means of three of these metrics, particularly the year 2013 which experienced high precipitation relative to the other 3 years of data. To quantify spatial and temporal dissimilarity among the samples over the 4-year study, we calculate pairwise squared-chord distances (SCD). The SCD values indicate higher compositional dissimilarity across the traps (0.38 mean) among all years than within a single trap from year to year (0.31 mean), suggesting that grassland vegetation can have different pollen signatures across finely sampled space and time, and emphasizing the need for additional long-term annual monitoring of grassland pollen

Genome-wide Linkage Scan to Identify Loci for Age at First Cigarette in Dutch Sibling Pairs

Most smokers begin smoking during adolescence and early age of smoking initiation is related to more frequent current smoking, daily smoking and more dependent smoking (Everret et al., 1999; Lando et al.

Quasi-two-dimensional acoustic metamaterial with negative bulk modulus

We present the experimental realization and characterization of an acoustic metamaterial with negative bulk modulus. The metamaterial consists of a two-dimensional array of cylindrical cavities, and the bulk modulus is controlled by their radius size and length. Experiments are performed in a two-dimensional waveguide where a slab of seven layers is used to extract the parameters of the metamaterial. A complete characterization of the constructed structure is reported, including the dispersion relation of the acoustic bands and the skin depth effect, which both have been measured, and the data are well supported by semianalytical models and by finite-element simulations. © 2012 American Physical Society.This work was supported by the Spanish MICINN under Contracts No. TEC2010-19751 and No. CSD2008-0066 (CONSOLIDER program), and by the USA Office of Naval Research. We acknowledge the technical help by A. Diaz-Rubio and A. Climente. J.S.-D. acknowledges useful discussions with A. Broatch and A. Krokhin. D.T. acknowledges the postdoctoral grant provided by the UPV under the program Campus de excelencia internacional.García Chocano, VM.; Graciá Salgado, R.; Torrent Martí, D.; Cervera Moreno, FS.; Sánchez-Dehesa Moreno-Cid, J. (2012). Quasi-two-dimensional acoustic metamaterial with negative bulk modulus. Physical Review B. 85(18). https://doi.org/10.1103/PhysRevB.85.184102S8518Fok, L., Ambati, M., & Zhang, X. (2008). Acoustic Metamaterials. MRS Bulletin, 33(10), 931-934. doi:10.1557/mrs2008.202Norris, A. N. (2009). Acoustic metafluids. The Journal of the Acoustical Society of America, 125(2), 839-849. doi:10.1121/1.3050288Liu, Z. (2000). Locally Resonant Sonic Materials. Science, 289(5485), 1734-1736. doi:10.1126/science.289.5485.1734Yang, Z., Mei, J., Yang, M., Chan, N. H., & Sheng, P. (2008). Membrane-Type Acoustic Metamaterial with Negative Dynamic Mass. Physical Review Letters, 101(20). doi:10.1103/physrevlett.101.204301Yao, S., Zhou, X., & Hu, G. (2008). Experimental study on negative effective mass in a 1D mass–spring system. New Journal of Physics, 10(4), 043020. doi:10.1088/1367-2630/10/4/043020Park, C. M., Park, J. J., Lee, S. H., Seo, Y. M., Kim, C. K., & Lee, S. H. (2011). Amplification of Acoustic Evanescent Waves Using Metamaterial Slabs. Physical Review Letters, 107(19). doi:10.1103/physrevlett.107.194301Fang, N., Xi, D., Xu, J., Ambati, M., Srituravanich, W., Sun, C., & Zhang, X. (2006). Ultrasonic metamaterials with negative modulus. Nature Materials, 5(6), 452-456. doi:10.1038/nmat1644Wang, Z. G., Lee, S. H., Kim, C. K., Park, C. M., Nahm, K., & Nikitov, S. A. (2008). Acoustic wave propagation in one-dimensional phononic crystals containing Helmholtz resonators. Journal of Applied Physics, 103(6), 064907. doi:10.1063/1.2894914Two-dimensional acoustic metamaterial with negative modulus. (2010). Journal of Applied Physics, 108(7), 074911. doi:10.1063/1.3493155Fey, J., & Robertson, W. M. (2011). Compact acoustic bandgap material based on a subwavelength collection of detuned Helmholtz resonators. Journal of Applied Physics, 109(11), 114903. doi:10.1063/1.3595677Li, J., & Chan, C. T. (2004). Double-negative acoustic metamaterial. Physical Review E, 70(5). doi:10.1103/physreve.70.055602Lee, S. H., Park, C. M., Seo, Y. M., Wang, Z. G., & Kim, C. K. (2010). Composite Acoustic Medium with Simultaneously Negative Density and Modulus. Physical Review Letters, 104(5). doi:10.1103/physrevlett.104.054301Torrent, D., & Sánchez-Dehesa, J. (2011). Multiple scattering formulation of two-dimensional acoustic and electromagnetic metamaterials. New Journal of Physics, 13(9), 093018. doi:10.1088/1367-2630/13/9/093018Torrent, D., & Sánchez-Dehesa, J. (2008). Anisotropic mass density by two-dimensional acoustic metamaterials. New Journal of Physics, 10(2), 023004. doi:10.1088/1367-2630/10/2/023004Pendry, J. B., & Li, J. (2008). An acoustic metafluid: realizing a broadband acoustic cloak. New Journal of Physics, 10(11), 115032. doi:10.1088/1367-2630/10/11/115032Torrent, D., & Sánchez-Dehesa, J. (2010). Anisotropic Mass Density by Radially Periodic Fluid Structures. Physical Review Letters, 105(17). doi:10.1103/physrevlett.105.174301Spiousas, I., Torrent, D., & Sánchez-Dehesa, J. (2011). Experimental realization of broadband tunable resonators based on anisotropic metafluids. Applied Physics Letters, 98(24), 244102. doi:10.1063/1.3599849Li, J., Fok, L., Yin, X., Bartal, G., & Zhang, X. (2009). Experimental demonstration of an acoustic magnifying hyperlens. Nature Materials, 8(12), 931-934. doi:10.1038/nmat2561Fokin, V., Ambati, M., Sun, C., & Zhang, X. (2007). Method for retrieving effective properties of locally resonant acoustic metamaterials. Physical Review B, 76(14). doi:10.1103/physrevb.76.144302Torrent, D., Håkansson, A., Cervera, F., & Sánchez-Dehesa, J. (2006). Homogenization of Two-Dimensional Clusters of Rigid Rods in Air. Physical Review Letters, 96(20). doi:10.1103/physrevlett.96.20430

Reproductive Factors and Serum Uric Acid Levels in Females from the General Population: The KORA F4 Study

Hyperuricemia is associated with an increased risk of metabolic and cardiovascular diseases. There are pronounced sex differences in the levels of uric acid. It is largely unknown whether or not reproductive parameters which induce hormonal changes are responsible for this. We examined if there are associations between reproductive parameters and uric acid levels in a female population-based sample. In this cross-sectional analysis, data of 1530 women aged 32 to 81 years participating in the KORA F4 study, conducted between 2006 and 2008 in Southern Germany were used. Reproductive parameters were obtained by standardized interviews. Uric acid levels were tested by the uricase method. The whole study sample and stratified in pre- and postmenopausal women was analyzed. Menopausal status and earlier age at menarche were associated with higher serum uric acid levels (age-adjusted: p-values 0.003, <0.001 respectively; after multivariable adjustment, including BMI: p-values 0.002, 0.036). A history of oral contraceptive use showed an association with uric acid levels only after multivariable adjustment (p-value 0.009). Hot flushes showed an association with uric acid levels only after age-adjustment (p-value 0.038), but lost significance after adding other confounders. Other reproductive factors, including parity, current or ever use of hormone replacement therapy, current use of oral contraceptives, hysterectomy, bilateral oophorectomy, or depressive mood related to menopausal transition were not associated with uric acid levels. Postmenopausal status, earlier age at menarche and a history of oral contraceptive use were independently associated with higher serum uric acid concentrations in women from the general population. Further studies, especially longitudinal population-based studies investigating the relationship of female reproductive parameters with uric acid levels are necessary to confirm our findings

Modulation of epithelial sodium channel (ENaC) expression in mouse lung infected with Pseudomonas aeruginosa

BACKGROUND: The intratracheal instillation of Pseudomonas aeruginosa entrapped in agar beads in the mouse lung leads to chronic lung infection in susceptible mouse strains. As the infection generates a strong inflammatory response with some lung edema, we tested if it could modulate the expression of genes involved in lung liquid clearance, such as the α, β and γ subunits of the epithelial sodium channel (ENaC) and the catalytic subunit of Na(+)-K(+)-ATPase. METHODS: Pseudomonas aeruginosa entrapped in agar beads were instilled in the lung of resistant (BalB/c) and susceptible (DBA/2, C57BL/6 and A/J) mouse strains. The mRNA expression of ENaC and Na(+)-K(+)-ATPase subunits was tested in the lung by Northern blot following a 3 hours to 14 days infection. RESULTS: The infection of the different mouse strains evoked regulation of α and β ENaC mRNA. Following Pseudomonas instillation, the expression of αENaC mRNA decreased to a median of 43% on days 3 and 7 after infection and was still decreased to a median of 45% 14 days after infection (p < 0.05). The relative expression of βENaC mRNA was transiently increased to a median of 241%, 24 h post-infection before decreasing to a median of 43% and 54% of control on days 3 and 7 post-infection (p < 0.05). No significant modulation of γENaC mRNA was detected although the general pattern of expression of the subunit was similar to α and β subunits. No modulation of α(1)Na(+)-K(+)-ATPase mRNA, the catalytic subunit of the sodium pump, was recorded. The distinctive expression profiles of the three subunits were not different, between the susceptible and resistant mouse strains. CONCLUSIONS: These results show that Pseudomonas infection, by modulating ENaC subunit expression, could influence edema formation and clearance in infected lungs

The early bee catches the flower - circadian rhythmicity influences learning performance in honey bees, Apis mellifera

Circadian rhythmicity plays an important role for many aspects of honey bees’ lives. However, the question whether it also affects learning and memory remained unanswered. To address this question, we studied the effect of circadian timing on olfactory learning and memory in honey bees Apis mellifera using the olfactory conditioning of the proboscis extension reflex paradigm. Bees were differentially conditioned to odours and tested for their odour learning at four different “Zeitgeber” time points. We show that learning behaviour is influenced by circadian timing. Honey bees perform best in the morning compared to the other times of day. Additionally, we found influences of the light condition bees were trained at on the olfactory learning. This circadian-mediated learning is independent from feeding times bees were entrained to, indicating an inherited and not acquired mechanism. We hypothesise that a co-evolutionary mechanism between the honey bee as a pollinator and plants might be the driving force for the evolution of the time-dependent learning abilities of bees

Disassembly and reassembly of human papillomavirus virus-like particles produces more virion-like antibody reactivity

<p>Abstract</p> <p>Background</p> <p>Human papillomavirus (HPV) vaccines based on major capsid protein L1 are licensed in over 100 countries to prevent HPV infections. The yeast-derived recombinant quadrivalent HPV L1 vaccine, GARDASIL(R), has played an important role in reducing cancer and genital warts since its introduction in 2006. The L1 proteins self-assemble into virus-like particles (VLPs).</p> <p>Results</p> <p>VLPs were subjected to post-purification disassembly and reassembly (D/R) treatment during bioprocessing to improve VLP immunoreactivity and stability. The post-D/R HPV16 VLPs and their complex with H16.V5 neutralizing antibody Fab fragments were visualized by cryo electron microscopy, showing VLPs densely decorated with antibody. Along with structural improvements, post-D/R VLPs showed markedly higher antigenicity to conformational and neutralizing monoclonal antibodies (mAbs) H16.V5, H16.E70 and H263.A2, whereas binding to mAbs recognizing linear epitopes (H16.J4, H16.O7, and H16.H5) was greatly reduced.</p> <p>Strikingly, post-D/R VLPs showed no detectable binding to H16.H5, indicating that the H16.H5 epitope is not accessible in fully assembled VLPs. An atomic homology model of the entire</p> <p>HPV16 VLP was generated based on previously determined high-resolution structures of bovine papillomavirus and HPV16 L1 pentameric capsomeres.</p> <p>Conclusions</p> <p>D/R treatment of HPV16 L1 VLPs produces more homogeneous VLPs with more virion-like antibody reactivity. These effects can be attributed to a combination of more complete and regular assembly of the VLPs, better folding of L1, reduced non-specific disulfide-mediated aggregation and increased stability of the VLPs. Markedly different antigenicity of HPV16 VLPs was observed upon D/R treatment with a panel of monoclonal antibodies targeting neutralization sensitive epitopes. Multiple epitope-specific assays with a panel of mAbs with different properties and epitopes are required to gain a better understanding of the immunochemical properties of VLPs and to correlate the observed changes at the molecular level. Mapping of known antibody epitopes to the homology model explains the changes in antibody reactivity upon D/R. In particular, the H16.H5 epitope is partially occluded by intercapsomeric interactions involving the L1 C-terminal arm. The homology model allows a more precise mapping of antibody epitopes. This work provides a better understanding of VLPs in current vaccines and could guide the design of improved vaccines or therapeutics.</p

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

BACKGROUND: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data was donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Efficient Allele-Specific Targeting of LRRK2 R1441 Mutations Mediated by RNAi

Since RNA interference (RNAi) has the potential to discriminate between single nucleotide changes, there is growing interest in the use of RNAi as a promising therapeutical approach to target dominant disease-associated alleles. Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been linked to dominantly inherited Parkinson's disease (PD). We focused on three LRRK2 mutations (R1441G/C and the more prevalent G2109S) hoping to identify shRNAs that would both recognize and efficiently silence the mutated alleles preferentially over the wild-type alleles. Using a luciferase-based reporter system, we identified shRNAs that were able to specifically target the R1441G and R1441C alleles with 80% silencing efficiency. The same shRNAs were able to silence specifically mRNAs encoding either partial or full-length mutant LRRK2 fusion proteins, while having a minimal effect on endogenous wild-type LRRK2 expression when transfected in 293FT cells. Shifting of the mutant recognition site (MRS) from position 11 to other sites (4 and 16, within the 19-mer window of our shRNA design) reduced specificity and overall silencing efficiency. Developing an allele-specific RNAi of G2019S was problematic. Placement of the MRS at position 10 resulted in efficient silencing of reporters (75–80%), but failed to discriminate between mutant and wild-type alleles. Shifting of the MRS to positions 4, 5, 15, 16 increased the specificity of the shRNAs, but reduced the overall silencing efficiency. Consistent with previous reports, these data confirm that MRS placement influences both allele-specificity and silencing strength of shRNAs, while further modification to hairpin design or MRS position may lead to the development of effective G2019S shRNAs. In summary, the effective shRNA against LRRK2 R1441 alleles described herein suggests that RNAi-based therapy of inherited Parkinson's disease is a viable approach towards developing effective therapeutic interventions for this serious neurodegenerative disease