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1.
J Environ Manage ; 233: 238-248, 2019 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-30580119

RESUMEN

The boreal forests of Alberta have extensive networks of legacy seismic exploration lines that have been linked to the decline of boreal woodland caribou (Rangifer tarandus caribou) populations throughout the region. In order to improve habitat quality for caribou, energy companies are investing significant resources in the restoration of many of these seismic lines in key areas, however, frequent large and intense wildfires may compromise the effectiveness of these conservation measures. To minimize the wildfire risk, managers need to know the likelihood of wildfire and the effectiveness of mitigation measures. We undertook a wildfire risk assessment across the Cold Lake caribou range where we used the Burn-P3 model to determine: a) burn probability; b) wildfire risk to restored seismic line areas; and c) the effectiveness of mitigation measures. The burn probability of the landscape was highly heterogeneous, and recent large burns and some waterbodies provided "shields" that reduced burn probability on their leeward sides. We designed mitigation scenarios to mimic the shielding effect of waterbodies and large recent burns by modeling the effects of increase suppression activity and fuel conversion within intensive management zones upwind of the resources to be protected. We found that these intensive management zones reduced the burn probability and wildfire hazard in the restored habitat areas but the effect declined rapidly as distance from the treatment zones increased. If land managers want to minimize the risk of losing their investments in caribou conservation to wildfire, it would be preferable to have mitigation measures spatially targeted closer to the conservation areas. Furthermore, it would be advisable to have redundancy in any conservation measures and wildfire-risk mitigations to ensure that losses due to wildfire on one area do not jeopardize all conservation projects within the landscape.


Asunto(s)
Quemaduras , Reno , Incendios Forestales , Alberta , Animales , Conservación de los Recursos Naturales , Probabilidad
2.
MethodsX ; 13: 102816, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39040216

RESUMEN

Wildfire is an important natural disturbance agent in Canadian forests, but it has also caused significant economic damage nationwide. Spatial fire growth models have emerged as important tools for representing wildfire dynamics across diverse landscapes, enabling the mapping of key wildfire hazard metrics such as location-specific burn probabilities or likelihoods of fire ignition. While these summary metrics have gained popularity, they often fall short in capturing the directional spread of wildfires and their potential spread distances. The metrics depicting the directional spread of wildfire can be derived from raw outputs generated with fire growth models, such as the perimeters and ignition locations of individual fires, but extracting this information requires complex data processing. To address this data gap, we present PostBP, an open-source Python package designed for post-processing the raw outputs of fire growth models - the ignition locations and perimeters of individual fires simulated over multiple stochastic iterations - into a matrix of fire spread likelihoods between all pairs of forest patches in a landscape. The PostBP also generates several other summary outputs, such as the source-sink ratio and the fire spread rose diagram. We provide an overview of PostBP's capabilities and demonstrate its practical application to a forested landscape.•Wildfire growth models generate large amounts of outputs, which are hard to summarize for practical decision-making.•The PostBP package calculates the summary metrics characterizing the directional spread of wildfires.•The fire risk summaries generated with PostBP can support the assessments of wildfire risk and mitigation measures.

3.
Mol Cell Biol ; 23(6): 1935-45, 2003 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-12612068

RESUMEN

The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5- or 10-bp gaps in the 3'-5' strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3'-5'-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.


Asunto(s)
Adenosina Trifosfatasas/fisiología , Cromatina/metabolismo , Proteínas de Drosophila/fisiología , Drosophila melanogaster/metabolismo , Adenosina Trifosfato/fisiología , Secuencias de Aminoácidos , Animales , Unión Competitiva , Catálisis , ADN/metabolismo , ADN/farmacología , ADN de Cadena Simple/metabolismo , ADN de Cadena Simple/farmacología , Activación Enzimática/efectos de los fármacos , Sustancias Macromoleculares , Conformación de Ácido Nucleico , Nucleosomas/metabolismo , Oligonucleótidos/metabolismo , Unión Proteica , Especificidad por Sustrato
4.
Biochem Soc Symp ; (73): 109-19, 2006.
Artículo en Inglés | MEDLINE | ID: mdl-16626292

RESUMEN

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.


Asunto(s)
Nucleosomas/genética , Nucleosomas/metabolismo , Adenosina Trifosfato/metabolismo , Sitios de Unión , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Ensamble y Desensamble de Cromatina , ADN/genética , ADN/metabolismo , Variación Genética , Histonas/genética , Histonas/metabolismo , Procesamiento Proteico-Postraduccional
6.
J Biol Chem ; 281(24): 16279-88, 2006 Jun 16.
Artículo en Inglés | MEDLINE | ID: mdl-16606615

RESUMEN

ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodeling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes but with different directionalities. We find that the yeast Isw1a, Isw2, and Chd1 enzymes preferentially move nucleosomes toward more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2, and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end, whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodeling by these enzymes.


Asunto(s)
Adenosina Trifosfatasas/fisiología , Proteínas de Unión al ADN/fisiología , Nucleosomas/metabolismo , Proteínas de Saccharomyces cerevisiae/fisiología , Saccharomyces cerevisiae/metabolismo , Adenosina Trifosfatasas/química , Animales , Cromatina/química , Ensamble y Desensamble de Cromatina , ADN/química , Proteínas de Unión al ADN/química , Nucleosomas/química , Proteínas de Saccharomyces cerevisiae/química , Factores de Transcripción/química , Xenopus laevis
7.
Mol Cell ; 21(3): 417-25, 2006 Feb 03.
Artículo en Inglés | MEDLINE | ID: mdl-16455496

RESUMEN

The Snf2 family represents a functionally diverse class of ATPase sharing the ability to modify DNA structure. Here, we use a magnetic trap and an atomic force microscope to monitor the activity of a member of this class: the RSC complex. This enzyme caused transient shortenings in DNA length involving translocation of typically 400 bp within 2 s, resulting in the formation of a loop whose size depended on both the force applied to the DNA and the ATP concentration. The majority of loops then decrease in size within a time similar to that with which they are formed, suggesting that the motor has the ability to reverse its direction. Loop formation was also associated with the generation of negative DNA supercoils. These observations support the idea that the ATPase motors of the Snf2 family of proteins act as DNA translocases specialized to generate transient distortions in DNA structure.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , ADN/química , Conformación de Ácido Nucleico , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/metabolismo , Adenosina Trifosfatasas/metabolismo , ADN/metabolismo , ADN/ultraestructura , ADN-Topoisomerasas/metabolismo , ADN Superhelicoidal/química , ADN Superhelicoidal/metabolismo , Sustancias Macromoleculares , Microscopía de Fuerza Atómica , Estrés Mecánico
8.
Biochemistry ; 44(29): 9899-904, 2005 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-16026162

RESUMEN

In the cell, DNA is wrapped on histone octamers, which reduces its accessibility for DNA interacting enzymes. We investigated de novo methylation of nucleosomal DNA in vitro and show that the Dnmt3a and Dnmt1 DNA methyltransferases efficiently methylate nucleosomal DNA without dissociation of the histone octamer from the DNA. In contrast, the prokaryotic SssI DNA methyltransferase and the catalytic domain of Dnmt3a are strongly inhibited by nucleosomes. We also found that full-length Dnmt1 and Dnmt3a bind to nucleosomes much stronger than their isolated catalytic domains, demonstrating that the N-terminal parts of the MTases are required for the interaction with nucleosomes. Variations of the DNA sequence or the histone tails did not significantly influence the methylation activity of Dnmt3a. The observation that mammalian methyltransferases directly modify nucleosomal DNA provides an insight into the mechanisms by which histone tail and DNA methylation patterns can influence each other because the DNA methylation pattern can be established while histones remain associated to the DNA.


Asunto(s)
ADN (Citosina-5-)-Metiltransferasas/química , Metilación de ADN , Nucleosomas/química , Animales , Secuencia de Bases , Sitios de Unión , Factor de Unión a CCCTC , Carboxiliasas , Catálisis , Dominio Catalítico , ADN (Citosina-5-)-Metiltransferasa 1 , ADN (Citosina-5-)-Metiltransferasas/metabolismo , ADN Metiltransferasa 3A , Proteínas de Unión al ADN/metabolismo , Histonas/metabolismo , Ratones , Datos de Secuencia Molecular , Nucleosomas/metabolismo , ARN Largo no Codificante , ARN no Traducido/metabolismo , Proteínas Represoras/metabolismo , Xenopus laevis
9.
Mol Cell ; 12(6): 1599-606, 2003 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-14690611

RESUMEN

ATP-dependent chromatin remodeling activities function to manipulate chromatin structure during gene regulation. One of the ways in which they do this is by altering the positions of nucleosomes along DNA. Here we provide support for the ability of these complexes to move nucleosomes into positions in which DNA is unraveled from one edge. This is expected to result in the loss of histone-DNA contacts that are important for retention of one H2A/H2B dimer within the nucleosome. Consistent with this we find that several chromatin remodeling complexes are capable of catalyzing the exchange of H2A/H2B dimers between chromatin fragments in an ATP-dependent reaction. This provides eukaryotes with additional means by which they may manipulate chromatin structure.


Asunto(s)
Adenosina Trifosfato/metabolismo , Cromatina/metabolismo , Histonas/metabolismo , Adenosina Trifosfatasas/metabolismo , Animales , Proteínas Cromosómicas no Histona/metabolismo , ADN de Hongos , Dimerización , Drosophila melanogaster , Proteínas Fúngicas/metabolismo , Modelos Moleculares , Conformación de Ácido Nucleico , Nucleosomas/metabolismo , Estructura Terciaria de Proteína , Factores de Transcripción/metabolismo , Xenopus laevis
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