Long-term changes of hydrogen-containing species in the stratosphere

Understanding the 1% per year increase of stratospheric water vapour from 1954 to 2000 is a great challenge in atmospheric science. The increase is predominantly caused by long-term changes in transport of water vapour into the stratosphere and systematic increases of tropospheric methane levels. This paper gives a review on stratospheric water vapour changes for the 1980 and 2000 time period with emphasis on the contribution of methane oxidation. Predictions for 2050 indicate that likely increases of tropospheric methane levels will lead to an increase of upper stratospheric water vapour values of about 0.4 ppmv. A similar value is predicted as an upper limit of effects of a future hydrogen economy. (c) 2006 Elsevier Ltd. All rights reserved

Technical Note: Reanalysis of upper troposphere humidity data from the MOZAIC programme for the period 1994 to 2009

In-situ observational data on the relative humidity (RH) in the upper troposphere and lowermost stratosphere (UT/LS), or tropopause region, respectively, collected aboard civil passenger aircraft in the MOZAIC (Measurements of OZone, water vapour, carbon monoxide and nitrogen oxides by in-service AIrbus airCraft) programme were reanalysed for the period 2000 to 2009. Previous analyses of probability distribution functions (PDF) of upper troposphere humidity (UTH) data from MOZAIC observations from year 2000 and later indicated a bias of UTH data towards higher RH values compared to data of the period 1994 to 1999. As a result, PDF of UTH data show a substantial fraction of observations above 100% relative humidity with respect to liquid water (RHliquid), which is not possible from thermodynamical principles. An in-depth reanalysis of the data set recovered a calibration artefact from year 2000 on, while data of the previous period from 1994 to 1999 were found to be correct. The full data set for 2000–2009 was reanalysed applying the adjusted calibration procedure. Applied correction schemes and a revised error analysis are presented along with the reanalysed PDF of RHliquid and RHice

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Background DNA shape analysis has demonstrated the potential to reveal structure-based mechanisms of protein–DNA binding. However, information about the influence of chemical modification of DNA is limited. Cytosine methylation, the most frequent modification, represents the addition of a methyl group at the major groove edge of the cytosine base. In mammalian genomes, cytosine methylation most frequently occurs at CpG dinucleotides. In addition to changing the chemical signature of C/G base pairs, cytosine methylation can affect DNA structure. Since the original discovery of DNA methylation, major efforts have been made to understand its effect from a sequence perspective. Compared to unmethylated DNA, however, little structural information is available for methylated DNA, due to the limited number of experimentally determined structures. To achieve a better mechanistic understanding of the effect of CpG methylation on local DNA structure, we developed a high-throughput method, methyl-DNAshape, for predicting the effect of cytosine methylation on DNA shape. Results Using our new method, we found that CpG methylation significantly altered local DNA shape. Four DNA shape features—helix twist, minor groove width, propeller twist, and roll—were considered in this analysis. Distinct distributions of effect size were observed for different features. Roll and propeller twist were the DNA shape features most strongly affected by CpG methylation with an effect size depending on the local sequence context. Methylation-induced changes in DNA shape were predictive of the measured rate of cleavage by DNase I and suggest a possible mechanism for some of the methylation sensitivities that were recently observed for human Pbx-Hox complexes. Conclusions CpG methylation is an important epigenetic mark in the mammalian genome. Understanding its role in protein–DNA recognition can further our knowledge of gene regulation. Our high-throughput methyl-DNAshape method can be used to predict the effect of cytosine methylation on DNA shape and its subsequent influence on protein–DNA interactions. This approach overcomes the limited availability of experimental DNA structures that contain 5-methylcytosine

Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.

Neuroendocrine (NE) cells use large dense core vesi-cles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secre-tory pathway. The dimmed (DIMM) basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, we have performed two in-dependent genome-wide analyses of DIMM’s activi-ties: (i) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of DIMM occupancy and (ii) deep sequencing of purified DIMM neurons to char-acterize their transcriptional profile. By this com-bined approach, we showed that DIMM binds to con-served E-boxes in enhancers of 212 genes whose expression is enriched in DIMM-expressing NE cells. DIMM binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical ma-chine learning revealed that flanking regions of puta-tive DIMM binding sites contribute to its DNA binding specificity. DIMM’s transcriptional repertoire features at least 20 LDCV constituents. In addition, DIMM no-tably targets the pro-secretory transcription factor, creb-A, but significantly, DIMM does not target any neuropeptide genes. DIMM therefore prescribes the scale of secretory activity in NE neurons, by a sys-tematic control of both proximal and distal points in the regulated secretory pathway

Validation of water vapour profiles (version 13) retrieved by the IMK/IAA scientific retrieval processor based on full resolution spectra measured by MIPAS on board Envisat

Vertical profiles of stratospheric water vapour measured by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) with the full resolution mode between September 2002 and March 2004 and retrieved with the IMK/IAA scientific retrieval processor were compared to a number of independent measurements in order to estimate the bias and to validate the existing precision estimates of the MIPAS data. The estimated precision for MIPAS is 5 to 10% in the stratosphere, depending on altitude, latitude, and season. The independent instruments were: the Halogen Occultation Experiment (HALOE), the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), the Improved Limb Atmospheric Spectrometer-II (ILAS-II), the Polar Ozone and Aerosol Measurement (POAM III) instrument, the Middle Atmospheric Water Vapour Radiometer (MIAWARA), the Michelson Interferometer for Passive Atmospheric Sounding, balloon-borne version (MIPAS-B), the Airborne Microwave Stratospheric Observing System (AMSOS), the Fluorescent Stratospheric Hygrometer for Balloon (FLASH-B), the NOAA frostpoint hygrometer, and the Fast In Situ Hygrometer (FISH). For the in-situ measurements and the ground based, air- and balloon borne remote sensing instruments, the measurements are restricted to central and northern Europe. The comparisons to satellite-borne instruments are predominantly at mid- to high latitudes on both hemispheres. In the stratosphere there is no clear indication of a bias in MIPAS data, because the independent measurements in some cases are drier and in some cases are moister than the MIPAS measurements. Compared to the infrared measurements of MIPAS, measurements in the ultraviolet and visible have a tendency to be high, whereas microwave measurements have a tendency to be low. The results of χ<sup>2</sup>-based precision validation are somewhat controversial among the comparison estimates. However, for comparison instruments whose error budget also includes errors due to uncertainties in spectrally interfering species and where good coincidences were found, the χ<sup>2</sup> values found are in the expected range or even below. This suggests that there is no evidence of systematically underestimated MIPAS random errors

Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA

We have investigated the anomalously weak binding of human papillomavirus (HPV) regulatory protein E2 to a DNA target containing the spacer sequence TATA. Experiments in magnesium (Mg2+) and calcium (Ca2+) ion buffers revealed a marked reduction in cutting by DNase I at the CpG sequence in the protein-binding site 3′ to the TATA spacer sequence, Studies of the cation dependence of DNA-E2 affinities showed that upon E2 binding the TATA sequence releases approximately twice as many Mg2+ ions as the average of the other spacer sequences. Binding experiments for TATA spacer relative to ATAT showed that in potassium ion (K+) the E2 affinity of the two sequences is nearly equal, but the relative dissociation constant (Kd) for TATA increases in the order K+ < Na+ < Ca2+ < Mg2+. Except for Mg2+, Kd for TATA relative to ATAT is independent of ion concentration, whereas for Mg2+ the affinity for TATA drops sharply as ion concentration increases. Thus, ions of increasing positive charge density increasingly distort the E2 binding site, weakening the affinity for protein. In the case of Mg2+, additional ions are bound to TATA that require displacement for protein binding. We suggest that the TATA sequence may bias the DNA structure towards a conformation that binds the protein relatively weakly

The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes

AmrZ, a member of the Ribbon-Helix-Helix family of DNA binding proteins, functions as both a transcriptional activator and repressor of multiple genes encoding Pseudomonas aeruginosa virulence factors. The expression of these virulence factors leads to chronic and sustained infections associated with worsening prognosis. In this study, we present the X-ray crystal structure of AmrZ in complex with DNA containing the repressor site, amrZ1. Binding of AmrZ to this site leads to auto-repression. AmrZ binds this DNA sequence as a dimer-of-dimers, and makes specific base contacts to two half sites, separated by a five base pair linker region. Analysis of the linker region shows a narrowing of the minor groove, causing significant distortions. AmrZ binding assays utilizing sequences containing variations in this linker region reveals that secondary structure of the DNA, conferred by the sequence of this region, is an important determinant in binding affinity. The results from these experiments allow for the creation of a model where both intrinsic structure of the DNA and specific nucleotide recognition are absolutely necessary for binding of the protein. We also examined AmrZ binding to the algD promoter, which results in activation of the alginate exopolysaccharide biosynthetic operon, and found the protein utilizes different interactions with this site. Finally, we tested the in vivo effects of this differential binding by switching the AmrZ binding site at algD, where it acts as an activator, for a repressor binding sequence and show that differences in binding alone do not affect transcriptional regulation

Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions

BACKGROUND: The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. METHODOLOGY/PRINCIPAL FINDINGS: The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR (31)P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The (31)P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. CONCLUSIONS/SIGNIFICANCE: The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions

Measuring Generalization of Visuomotor Perturbations in Wrist Movements Using Mobile Phones

Recent studies in motor control have shown that visuomotor rotations for reaching have narrow generalization functions: what we learn during movements in one direction only affects subsequent movements into close directions. Here we wanted to measure the generalization functions for wrist movement. To do so we had 7 subjects performing an experiment holding a mobile phone in their dominant hand. The mobile phone's built in acceleration sensor provided a convenient way to measure wrist movements and to run the behavioral protocol. Subjects moved a cursor on the screen by tilting the phone. Movements on the screen toward the training target were rotated and we then measured how learning of the rotation in the training direction affected subsequent movements in other directions. We find that generalization is local and similar to generalization patterns of visuomotor rotation for reaching