348 research outputs found
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
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations
Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein–DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein–DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein–DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.National Institutes of Health [R01GM106056 to R.R., T.D.T.; U54CA121852 in part to T.D.T.]; Boston University Undergraduate Research Opportunities Program [Faculty Matching Grants to D.O. and Y.J.]; USC Graduate School [Research Enhancement Fellowship and Manning Endowed Fellowship to T.P.C.]. R.R. is an Alfred P. Sloan Research Fellow. Funding for open access charge: Boston University. (R01GM106056 - National Institutes of Health; U54CA121852 - National Institutes of Health; Boston University Undergraduate Research Opportunities Program; USC Graduate School; Boston University)https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1Published versio
Digitization bolstering self-directed learning for information literate adults – a systematic review
Learning skills are fundamental 21st century skills that enable people to thrive in an increasingly uncertain future. Digitization and the current COVID-19 pandemic have been key drivers of uncertainty and changing conditions. In the face of change and uncertainty, self-directed learning is a fundamental competence. However, to date there is a dearth of understanding regarding how digital technologies are supporting or affecting self-directed learning in adulthood. In order to address this, the objective of the present study was to examine through a systematic literature review what is known to date regarding – how can digital technologies support self-directed learning in adult learning and education? The novel findings of the present study suggest digitization has transformed opportunities for self-directed learning in informal, non-formal, and in formal educational settings. However, a key finding of this present study was that the affordances of digital technologies might be described as a double edged sword: (1) digital technologies provide convenient accessibility to information, which acts as an enabler of self-directed learning; but (2) the increasing volume of available information demands additional learner skill in information literacy – part of being a competent self-directed learner – in order to navigate information in a meaningful way. These two concomitant phenomena might in part explain the widening digital divide that has been recorded in recent years
Global aviation contrail climate effects from 2019 to 2021
The global annual mean radiative forcing (RF) attributable to contrail cirrus is comparable to the RF from aviation’s cumulative CO2 emissions. Here, we simulate the global contrail climate forcing for 2019–2021 using reanalysis weather data and improved engine emission estimates along actual flight trajectories derived from Automatic Dependent Surveillance–Broadcast telemetry. Our 2019 global annual mean contrail net RF (62.1 mW m-2) is 44 % lower than current best estimates for 2018 (111 [33, 189] mW m-2). Regionally, the contrail net RF is largest over Europe (876 mW m-2) and the US (414 mW m-2), while the RF over East Asia (64 mW m-2) and China (62 mW m-2) are close to the global mean value because fewer flights in these regions form contrails as a result of lower cruise altitudes and limited ice supersaturated regions in the subtropics due to the Hadley Circulation. Globally, COVID-19 reduced the flight distance flown and contrail net RF in 2020 (-43 % and -56 % respectively vs. 2019) and 2021 (-31 % and -49 % respectively) with significant regional variation. Around 14 % of all flights form a contrail with a net warming effect, yet only 2 % of all flights account for 80 % of the annual contrail energy forcing. The spatiotemporal patterns of the most strongly warming and cooling contrail segments can be attributed to flight scheduling factors, aircraft–engine particle number emissions, tropopause height, background cloud and radiation fields, and albedo. Our contrail RF estimates are most sensitive to corrections applied to the global humidity fields, followed by assumptions on the aircraft-engine particle number emissions, and is least sensitive to radiative heating effects on the contrail plume and contrail-contrail overlapping. Accounting for the sensitivity analysis, we estimate a 2019 global contrail net RF of 62.1 [34.8, 74.8] mW m-2
Zinc is essential for high-affinity DNA binding and recombinase activity of φC31 integrase
The mechanism through which the large serine recombinases bind DNA is poorly understood. Alignments of ϕC31 integrase (Int) and its relatives indicate the presence of a conserved motif containing four cysteines resembling a zinc finger. Inductively coupled plasma–mass spectrometry (ICP–MS) confirmed that an Int monomer contains one atom of zinc. Pre-incubation of Int with ethylenediaminetetraacetic acid (EDTA) was detrimental for both recombination activity and DNA binding affinities but full activity could be restored by adding back Zn2+. Mutations in the cysteines and other highly conserved residues yielded proteins that were hypersensitive to proteases, suggesting that without zinc the domain is unfolded. Substitutions in the highly charged region between the conserved cysteines led to lowered DNA binding affinities while circular dichroism revealed that these variant Ints were not greatly affected in overall folding. Int was protected from inhibition by EDTA when DNA containing an attachment site was present suggesting that the zinc finger and the DNA are in close proximity. A truncated mutant of Int, hInt V371SUGA, lacking the putative zinc finger could bind DNA with low affinity. The data are consistent with there being at least two DNA binding motifs in Int one of which is the zinc finger-like motif
The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding
SimR, a TetR-family transcriptional regulator (TFR), controls the export of simocyclinone, a potent DNA gyrase inhibitor made by Streptomyces antibioticus. Simocyclinone is exported by a specific efflux pump, SimX and the transcription of simX is repressed by SimR, which binds to two operators in the simR-simX intergenic region. The DNA-binding domain of SimR has a classical helix-turn-helix motif, but it also carries an arginine-rich N-terminal extension. Previous structural studies showed that the N-terminal extension is disordered in the absence of DNA. Here, we show that the N-terminal extension is sensitive to protease cleavage, but becomes protease resistant upon binding DNA. We demonstrate by deletion analysis that the extension contributes to DNA binding, and describe the crystal structure of SimR bound to its operator sequence, revealing that the N-terminal extension binds in the minor groove. In addition, SimR makes a number of sequence-specific contacts to the major groove via its helix-turn-helix motif. Bioinformatic analysis shows that an N-terminal extension rich in positively charged residues is a feature of the majority of TFRs. Comparison of the SimR–DNA and SimR–simocyclinone complexes reveals that the conformational changes associated with ligand-mediated derepression result primarily from rigid-body rotation of the subunits about the dimer interface
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
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine•pyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov
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