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1.
Mikkel Nissum Jens-Jakob Karlsson Jens Ulstrup Palle Waage Jensen G. Smulevich 《Journal of biological inorganic chemistry》1997,2(3):302-307
Di-heme Pseudomonas stutzeri cytochrome c
4 has been characterized by electronic absorption and resonance Raman spectroscopies in the ferric and ferrous forms at pH 7.5
and at room temperature. The data indicate that the two hemes are inequivalent. It is proposed that the N-terminal contains
a more relaxed heme as a consequence of the relative orientation of the methionine and histidine ligands with respect to the
N-Fe-N directions of the heme plane. This causes a weakening of the Fe-S bond with concomitant partial dissociation of the
methionine and the formation of an Fe-aquo bond. Heme group relaxation is further accompanied by less distortion of the heme
group than that associated with cytochrome c, expansion of the "core" and a negative shift of the redox potential.
Received: 17 December 1996 / Accepted: 6 March 1997 相似文献
2.
Torbern Tagesson Meelis Mölder Mikhail Mastepanov Charlotte Sigsgaard Mikkel P. Tamstorf Magnus Lund Julie M. Falk Anders Lindroth Torben R. Christensen Lena Ström 《Global Change Biology》2012,18(6):1928-1940
The land‐atmosphere exchange of methane (CH4) and carbon dioxide (CO2) in a high‐Arctic wet tundra ecosystem (Rylekærene) in Zackenberg, north‐eastern Greenland, was studied over the full growing season and until early winter in 2008 and from before snow melt until early winter in 2009. The eddy covariance technique was used to estimate CO2 fluxes and a combination of the gradient and eddy covariance methods was used to estimate CH4 fluxes. Small CH4 bursts were observed during spring thawing 2009, but these existed during short periods and would not have any significant effect on the annual budget. Growing season CH4 fluxes were well correlated with soil temperature, gross primary production, and active layer thickness. The CH4 fluxes remained low during the entire autumn, and until early winter. No increase in CH4 fluxes were seen as the soil started to freeze. However, in autumn 2008 there were two CH4 burst events that were highly correlated with atmospheric turbulence. They were likely associated with the release of stored CH4 from soil and vegetation cavities. Over the measurement period, 7.6 and 6.5 g C m?2 was emitted as CH4 in 2008 and in 2009, respectively. Rylekærene acted as a C source during the warmer and wetter measurement period 2008, whereas it was a C sink for the colder and drier period of 2009. Wet tundra ecosystems, such as Rylekærene may thus play a more significant role for the climate in the future, as temperature and precipitation are predicted to increase in the high‐Arctic. 相似文献
3.
Schubert M Ginolhac A Lindgreen S Thompson JF Al-Rasheid KA Willerslev E Krogh A Orlando L 《BMC genomics》2012,13(1):178
ABSTRACT: BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material. 相似文献
4.
Joan Thiesen Torben S. Christensen Thomas G. Kristensen Rikke D. Andersen Brit Brunoe Trine K. Gregersen Mikkel Thrane Bo P. Weidema 《The International Journal of Life Cycle Assessment》2008,13(2):104-114
Goal, Scope and Background Traditionally, comparative life cycle assessments (LCA) have not considered rebound effects, for instance in case of significant
price differences among the compared products. No justifications have been made for this delimitation in scope. This article
shows that price differences and the consequent effects of marginal consumer expenditure may influence the conclusions of
comparative LCA significantly. We also show that considerations about rebound effects of price differences can be included
in LCAs.
Methods The direct rebound effect of a price difference is marginal consumption. Based on statistical data on private consumption
in different income groups (Statistics Denmark 2005a, 2005b), the present article provides an estimate of how an average Danish
household will spend an additional 1 DKK for further consumer goods, when the household has gained money from choosing a cheaper
product alternative. The approach is to use marginal income changes and the following changes in consumption patterns as an
expression for marginal consumption. Secondly, the environmental impact potentials related to this marginal consumption are
estimated by the use of environmental impact intensity data from an IO-LCA database (Weidema et al. 2005). Finally, it is
discussed whether, and in which ways the conclusions of comparative LCAs can be affected by including the price difference
between product alternatives. This is elucidated in a case study of a comparative LCA screening of two different kinds of
Danish cheese products (Fricke et al. 2004).
Results Car purchase and driving, use and maintenance of dwelling, clothing purchase and insurance constitutes the largest percentages
of the marginal consumption. In a case study of two cheeses, the including the impact potentials related to the price difference
results in significant changes in the total impact potentials. Considering the relatively small price difference of the two
products, it is likely also to have a significant influence on the results of comparative LCAs more generally.
Discussion The influence of marginal consumption in comparative LCAs is relevant to consider in situations with large differences in
the price of the product alternatives being compared, and in situations with minor differences in the impact potentials related
to the alternatives. However, different uncertainties are linked to determining the pattern for marginal consumption and the
environmental impact potential related to this. These are first of all related to the method used, but also include inaccurate
data of consumption in households, aggregation and weighting of income groups, aggregation of product groups, estimation and
size of the price difference, and the general applicability of the results.
Conclusion Incorporating marginal consumption in consequential LCAs is possible in practice. In the case study used, including the rebound
effects of the price difference has a significant influence on the result of the comparative LCA, as the result for the impact
categories acidification and nutrient enrichment changes in favour of the expensive product.
Recommendations and Perspectives It is recommended that the rebound effects of price differences should be included more frequently in LCAs. In order to ensure
this, further research in marginal consumption and investment patterns and IO data for different countries or regions is required.
Furthermore, this study does not consider the economic distributional consequences of buying an expensive product instead
of a cheaper product (e.g. related to how the profit is spent by those who provided the product). It should also be noted,
that more expensive products not necessarily result in less consumption, as those who provided the product also will spend
the money they have earned from the sale. Ideally, these consequences should also be further investigated. Likewise, the development
of databases to include marginal consumption in PC-tools is needed. In general, considerations of marginal consumption would
favour expensive product alternatives, depending, however, on the type of consumer.
ESS-Submission Editor: Dr. David Hunkeler (david.hunkeler@aquaplustech.ch) 相似文献
5.
Peter Hammershøj Mikkel Jessing Anders Ø. Madsen Knud J. Jensen Jørn B. Christensen Ulrik Boas 《International journal of peptide research and therapeutics》2007,13(1-2):209-212
The development of new linkers (handles) for solid-phase synthesis provides new chemical opportunities for peptide synthesis.
To understand the chemical properties of a recently developed backbone amide linker from a structural perspective, the crystal
structure of S-((5-formyl-3,4-ethylenedioxy)thiophene-2-yl)-3-thiopropionic acid (T-BAL2) was studied. Specifically, we wished
to address whether this highly substituted thiophene retained planarity in the aromatic ring as well as between the aromatic
ring and the aldehyde carbonyl. Furthermore, we sought an explanation for the relatively low reactivity in reductive aminations
of the thienylaldehyde with amines in solution and on solid phase. Based on the crystal structure of T-BAL2, the thienyl-C
(aldehyde) and C–O (aldehyde) bond lengths were applied as measures for the electron-deficiency (electrophilicity) of the
aldehyde and compared to similar bond lengths found in previously reported formylated homo- and hetero-aromatic systems, which
show significantly higher reactivity towards imine formation. The bond lengths found in the present structure are in accordance
with normal C–C single bond and C–O double bond lengths. The high similarity in aldehyde bond lengths in the present system
and in the reported systems indicates similar electron distribution in these systems. The lower reactivity of the present
system may therefore not be attributed to electronic factors. 相似文献
6.
Stefanie Wagner Frédéric Lagane Andaine Seguin‐Orlando Mikkel Schubert Thibault Leroy Erwan Guichoux Emilie Chancerel Inger Bech‐Hebelstrup Vincent Bernard Cyrille Billard Yves Billaud Matthias Bolliger Christophe Croutsch Katarina Čufar Frédérique Eynaud Karl Uwe Heussner Joachim Köninger Fabien Langenegger Frédéric Leroy Christine Lima Nicoletta Martinelli Garry Momber André Billamboz Oliver Nelle Antoni Palomo Raquel Piqué Marianne Ramstein Roswitha Schweichel Harald Stäuble Willy Tegel Xavier Terradas Florence Verdin Christophe Plomion Antoine Kremer Ludovic Orlando 《Molecular ecology》2018,27(5):1138-1154
Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management. 相似文献
7.
Alba Rey‐Iglesia Shyam Gopalakrishan Christian Care David E. Alquezar‐Planas Anne Ahlmann Nielsen Timo Rder Lene Bruhn Pedersen Christina Nsborg‐Nielsen Mikkel‐Holger S. Sinding Martin Fredensborg Rath Zhipeng Li Bent Petersen M. Thomas P. Gilbert Michael Bunce Tobias Mourier Anders Johannes Hansen 《Molecular ecology resources》2019,19(2):512-525
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome‐scale studies to characterize both model and non‐model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome‐wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site‐associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms—enabling the exploration of diverse evolutionary and conservation questions. 相似文献
8.
Mosbacher Jesper Bruun Michelsen Anders Stelvig Mikkel Hjermstad-Sollerud Håvard Schmidt Niels Martin 《Ecosystems》2019,22(5):1095-1107
Ecosystems - Herbivores are key drivers of vegetation dynamics in most ecosystems. However, the effect of high arctic herbivores on vegetation dynamics throughout a growing season is not well... 相似文献
9.
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model 下载免费PDF全文
The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient. 相似文献
10.
Armelin Vinicius Araújo Thomsen Mikkel Thy Teixeira Mariana Teodoro Florindo Luiz Henrique Bayley Mark Wang Tobias 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》2019,189(3-4):425-440
Journal of Comparative Physiology B - All vertebrates possess baroreceptors monitoring arterial blood pressure and eliciting reflexive changes in vascular resistance and heart rate in response to... 相似文献