Evaluation of PCR primer selectivity and phylogenetic specificity by using amplification of 16S rRNA genes from betaproteobacterial ammonia-oxidizing bacteria in environmental samples

The effect of primer specificity for studying the diversity of ammonia-oxidizing betaproteobacteria (βAOB) was evaluated. βAOB represent a group of phylogenetically related organisms for which the 16S rRNA gene approach is especially suitable. We used experimental comparisons of primer performance with water samples, together with an in silico analysis of published sequences and a literature review of clone libraries made with four specific PCR primers for the βAOB 16S rRNA gene. With four aquatic samples, the primers NitA/NitB produced the highest frequency of ammonia-oxidizing-bacterium-like sequences compared to clone libraries with products amplified with the primer combinations βAMOf/βAMOr, βAMOf/Nso1255g, and NitA/Nso1225g. Both the experimental examination of ammonia-oxidizing-bacterium-specific 16S rRNA gene primers and the literature search showed that neither specificity nor sensitivity of primer combinations can be evaluated reliably only by sequence comparison. Apparently, the combination of sequence comparison and experimental data is the best approach to detect possible biases of PCR primers. Although this study focused on βAOB, the results presented here more generally exemplify the importance of primer selection and potential primer bias when analyzing microbial communities in environmental samples

Minimal recipes for global cloudiness

Clouds are primary modulators of Earth’s energy balance. It is thus important to understand the links connecting variabilities in cloudiness to variabilities in other state variables of the climate system, and also describe how these links would change in a changing climate. A conceptual model of global cloudiness can help elucidate these points. In this work we derive simple representations of cloudiness, that can be useful in creating a theory of global cloudiness. These representations illustrate how both spatial and temporal variability of cloudiness can be expressed in terms of basic state variables. Specifically, cloud albedo is captured by a nonlinear combination of pressure velocity and a measure of the low-level stability, and cloud longwave effect is captured by surface temperature, pressure velocity, and standard deviation of pressure velocity. We conclude with a short discussion on the usefulness of this work in the context of global warming response studies

Maintaining real-time precise point positioning during outages of orbit and clock corrections

The precise point positioning (PPP) is a popular positioning technique that is dependent on the use of precise orbits and clock corrections. One serious problem for real-time PPP applications such as natural hazard early warning systems and hydrographic surveying is when a sudden communication break takes place resulting in a discontinuity in receiving these orbit and clock corrections for a period that may extend from a few minutes to hours. A method is presented to maintain real-time PPP with 3D accuracy less than a decimeter when such a break takes place. We focus on the open-access International GNSS Service (IGS) real-time service (RTS) products and propose predicting the precise orbit and clock corrections as time series. For a short corrections outage of a few minutes, we predict the IGS-RTS orbits using a high-order polynomial, and for longer outages up to 3 h, the most recent IGS ultra-rapid orbits are used. The IGS-RTS clock corrections are predicted using a second-order polynomial and sinusoidal terms. The model parameters are estimated sequentially using a sliding time window such that they are available when needed. The prediction model of the clock correction is built based on the analysis of their properties, including their temporal behavior and stability. Evaluation of the proposed method in static and kinematic testing shows that positioning precision of less than 10 cm can be maintained for up to 2 h after the break. When PPP re-initialization is needed during the break, the solution convergence time increases; however, positioning precision remains less than a decimeter after convergence

Unintentional high density p-type modulation doping of a GaAs/AlAs core-multi-shell nanowire

Achieving significant doping in GaAs/AlAs core/shell nanowires (NWs) is of considerable technological importance but remains a challenge due to the amphoteric behavior of the dopant atoms. Here we show that placing a narrow GaAs quantum well in the AlAs shell effectively getters residual carbon acceptors leading to an \emph{unintentional} p-type doping. Magneto-optical studies of such a GaAs/AlAs core multi-shell NW reveal quantum confined emission. Theoretical calculations of NW electronic structure confirm quantum confinement of carriers at the core/shell interface due to the presence of ionized carbon acceptors in the 1~nm GaAs layer in the shell. Micro-photoluminescence in high magnetic field shows a clear signature of avoided crossings of the $n=0$ Landau level emission line with the $n=2$ Landau level TO phonon replica. The coupling is caused by the resonant hole-phonon interaction, which points to a large 2D hole density in the structure.Comment: just published in Nano Letters (http://pubs.acs.org/doi/full/10.1021/nl500818k

Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria)

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 6 (2012): 670–679, doi:10.1038/ismej.2011.128.Akinetes are dormancy cells commonly found among filamentous cyanobacteria, many of which are toxic and/or nuisance, bloom-forming species. Development of akinetes from vegetative cells is a process that involves morphological and biochemical modifications. Here we applied a single cell approach to quantify genome and ribosome content of akinetes and vegetative cells in Aphanizomenon ovalisporum (Cyanobacteria). Vegetative cells of A. ovalisporum were naturally polyploid and contained on average 8 genome copies per cell. However, the chromosomal content of akinetes increased up to 450 copies, with an average value of 119 genome copies per akinete, 15 fold higher that in vegetative cells. Based on fluorescence in situ hybridization with a probe targeting 16S rRNA and detection with confocal laser scanning microscopy we conclude that ribosomes accumulated in akinetes to a higher level than that found in vegetative cells. We further present evidence that this massive accumulation of nucleic acids in akinetes is likely supported by phosphate supplied from inorganic polyphosphate bodies that were abundantly present in vegetative cells, but notably absent from akinetes. These results are interpreted in the context of cellular investments for proliferation following long term dormancy, as the high nucleic acid content would provide the basis for extended survival, rapid resumption of metabolic activity and cell division upon germination.Supported by the Gruss Lipper Foundation research award (AS). This study was part of the Joint German-Israeli-Project (FKZ 02WT0985, WR803) funded by the German Ministry of Research and Technology (BMBF) and Israel Ministry of Science and Technology (MOST)

Phosphatidylserine Increases IKBKAP Levels in Familial Dysautonomia Cells

Familial Dysautonomia (FD) is an autosomal recessive congenital neuropathy that results from abnormal development and progressive degeneration of the sensory and autonomic nervous system. The mutation observed in almost all FD patients is a point mutation at position 6 of intron 20 of the IKBKAP gene; this gene encodes the IκB kinase complex-associated protein (IKAP). The mutation results in a tissue-specific splicing defect: Exon 20 is skipped, leading to reduced IKAP protein expression. Here we show that phosphatidylserine (PS), an FDA-approved food supplement, increased IKAP mRNA levels in cells derived from FD patients. Long-term treatment with PS led to a significant increase in IKAP protein levels in these cells. A conjugate of PS and an omega-3 fatty acid also increased IKAP mRNA levels. Furthermore, PS treatment released FD cells from cell cycle arrest and up-regulated a significant number of genes involved in cell cycle regulation. Our results suggest that PS has potential for use as a therapeutic agent for FD. Understanding its mechanism of action may reveal the mechanism underlying the FD disease

Environmental risk assessments for transgenic crops producing output trait enzymes

The environmental risks from cultivating crops producing output trait enzymes can be rigorously assessed by testing conservative risk hypotheses of no harm to endpoints such as the abundance of wildlife, crop yield and the rate of degradation of crop residues in soil. These hypotheses can be tested with data from many sources, including evaluations of the agronomic performance and nutritional quality of the crop made during product development, and information from the scientific literature on the mode-of-action, taxonomic distribution and environmental fate of the enzyme. Few, if any, specific ecotoxicology or environmental fate studies are needed. The effective use of existing data means that regulatory decision-making, to which an environmental risk assessment provides essential information, is not unnecessarily complicated by evaluation of large amounts of new data that provide negligible improvement in the characterization of risk, and that may delay environmental benefits offered by transgenic crops containing output trait enzymes