774 research outputs found
The role of active movement in fungal ecology and community assembly
Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth, mycelial translocations, or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus
Facilitated diffusion of DNA-binding proteins
The diffusion-controlled limit of reaction times for site-specific
DNA-binding proteins is derived from first principles. We follow the generally
accepted concept that a protein propagates via two competitive modes, a
three-dimensional diffusion in space and a one-dimensional sliding along the
DNA. However, our theoretical treatment of the problem is new. The accuracy of
our analytical model is verified by numerical simulations. The results confirm
that the unspecific binding of protein to DNA, combined with sliding, is
capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR
Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody
BACKGROUND: Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examined with the application of histone PTM-specific antibodies. In spite of their central role in chromatin research, polyclonal antibodies suffer from disadvantages like batch-to-batch variability and insufficient documentation of their quality and specificity. RESULTS: To mitigate some of the pitfalls of using polyclonal antibodies against H3K4me3, we successfully validated the application of a recombinant TAF3 PHD domain as anti-H3K4me3 affinity reagent in peptide array, western blot and ChIP-like experiments coupled with qPCR and deep sequencing. CONCLUSIONS: The successful addition of the TAF3 PHD domain to the growing catalog of recombinant affinity reagents for histone PTMs could help to improve the reproducibility, interpretation and cross-laboratory validation of chromatin data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0061-9) contains supplementary material, which is available to authorized users
VEGF guides angiogenic sprouting utilizing endothelial tip cell filopodia
Vascular endothelial growth factor (VEGF-A) is a major regulator of blood vessel formation and function. it controls several processes in endothelial cells, such as proliferation, survival, and migration, but it is not known how these are coordinately regulated to result in more complex morphogenetic events, such as tubular sprouting, fusion, and network formation. We show here that VEGF-A controls angiogenic sprouting in the early postnatal retina by guiding filopodial extension from specialized endothelial cells situated at the tips of the vascular sprouts. The tip cells respond to VEGF-A only by guided migration; the proliferative response to VEGF-A occurs in the sprout stalks. These two cellular responses are both mediated by agonistic activity of VEGF-A on VEGF receptor 2. Whereas tip cell migration depends on a gradient of VEGF-A, proliferation is regulated by its concentration. Thus, vessel patterning during retinal angiogenesis depends on the balance between two different qualities of the extracellular VEGF-A distribution, which regulate distinct cellular responses in defined populations of endothelial cells
Current models broadly neglect specific needs of biodiversity conservation in protected areas under climate change
<p>Abstract</p> <p>Background</p> <p>Protected areas are the most common and important instrument for the conservation of biological diversity and are called for under the United Nations' <it>Convention on Biological Diversity</it>. Growing human population densities, intensified land-use, invasive species and increasing habitat fragmentation threaten ecosystems worldwide and protected areas are often the only refuge for endangered species. Climate change is posing an additional threat that may also impact ecosystems currently under protection. Therefore, it is of crucial importance to include the potential impact of climate change when designing future nature conservation strategies and implementing protected area management. This approach would go beyond reactive crisis management and, by necessity, would include anticipatory risk assessments. One avenue for doing so is being provided by simulation models that take advantage of the increase in computing capacity and performance that has occurred over the last two decades.</p> <p>Here we review the literature to determine the state-of-the-art in modeling terrestrial protected areas under climate change, with the aim of evaluating and detecting trends and gaps in the current approaches being employed, as well as to provide a useful overview and guidelines for future research.</p> <p>Results</p> <p>Most studies apply statistical, bioclimatic envelope models and focus primarily on plant species as compared to other taxa. Very few studies utilize a mechanistic, process-based approach and none examine biotic interactions like predation and competition. Important factors like land-use, habitat fragmentation, invasion and dispersal are rarely incorporated, restricting the informative value of the resulting predictions considerably.</p> <p>Conclusion</p> <p>The general impression that emerges is that biodiversity conservation in protected areas could benefit from the application of modern modeling approaches to a greater extent than is currently reflected in the scientific literature. It is particularly true that existing models have been underutilized in testing different management options under climate change. Based on these findings we suggest a strategic framework for more effectively incorporating the impact of climate change in models exploring the effectiveness of protected areas.</p
DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation.
Specific DNA methylation at CpG and non-CpG sites is essential for chromatin regulation. The DNA methyltransferase DNMT3A interacts with target sites surrounded by variable DNA sequences with its TRD and RD loops, but the functional necessity of these interactions is unclear. We investigated CpG and non-CpG methylation in a randomized sequence context using WT DNMT3A and several DNMT3A variants containing mutations at DNA-interacting residues. Our data revealed that the flanking sequence of target sites between theĀ -2 and up to theĀ +8 position modulates methylation rates >100-fold. Non-CpG methylation flanking preferences were even stronger and favor C(+1). R836 and N838 in concert mediate recognition of the CpG guanine. R836 changes its conformation in a flanking sequence-dependent manner and either contacts the CpG guanine or theĀ +1/+2 flank, thereby coupling the interaction with both sequence elements. R836 suppresses activity at CNT sites but supports methylation of CAC substrates, the preferred target for non-CpG methylation of DNMT3A in cells. N838 helps to balance this effect and prevent the preference for C(+1) from becoming too strong. Surprisingly, we found L883 reduces DNMT3A activity despite being highly conserved in evolution. However, mutations at L883 disrupt the DNMT3A-specific DNA interactions of the RD loop, leading to altered flanking sequence preferences. Similar effects occur after the R882H mutation in cancer cells. Our data reveal that DNMT3A forms flexible and interdependent interaction networks with the CpG guanine and flanking residues that ensure recognition of the CpG and efficient methylation of the cytosine in contexts of variable flanking sequences
Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites
Surviving in a diverse environment requires corresponding organism responses.
At the cellular level, such adjustment relies on the transcription factors
(TFs) which must rapidly find their target sequences amidst a vast amount of
non-relevant sequences on DNA molecules. Whether these transcription factors
locate their target sites through a 1D or 3D pathway is still a matter of
speculation. It has been suggested that the optimum search time is when the
protein equally shares its search time between 1D and 3D diffusions. In this
paper, we study the above problem using a Monte Carlo simulation by considering
a very simple physical model. A 1D strip, representing a DNA, with a number of
low affinity sites, corresponding to non-target sites, and high affinity sites,
corresponding to target sites, is considered and later extended to a 2D strip.
We study the 1D and 3D exploration pathways, and combinations of the two modes
by considering three different types of molecules: a walker that randomly walks
along the strip with no dissociation; a jumper that represents dissociation and
then re-association of a TF with the strip at later time at a distant site; and
a hopper that is similar to the jumper but it dissociates and then
re-associates at a faster rate than the jumper. We analyze the final
probability distribution of molecules for each case and find that TFs can
locate their targets fast enough even if they spend 15% of their search time
diffusing freely in the solution. This indeed agrees with recent experimental
results obtained by Elf et al. 2007 and is in contrast with theoretical
expectation.Comment: 24 pages, 9 figure
The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner
The specificity and processivity of DNA methyltransferases have important implications regarding their biological functions. We have investigated the sequence specificity of CcrM and show here that the enzyme has a high specificity for GANTC sites, with only minor preferences at the central position. It slightly prefers hemimethylated DNA, which represents the physiological substrate. In a previous work, CcrM was reported to be highly processive [Berdis et al. (1998) Proc. Natl Acad. Sci. USA
95: 2874ā2879]. However upon review of this work, we identified a technical error in the setup of a crucial experiment in this publication, which prohibits making any statement about the processivity of CcrM. In this study, we performed a series of in vitro experiments to study CcrM processivity. We show that it distributively methylates six target sites on the pUC19 plasmid as well as two target sites located on a 129-mer DNA fragment both in unmethylated and hemimethylated state. Reaction quenching experiments confirmed the lack of processivity. We conclude that the original statement that CcrM is processive is no longer valid
Temporal Stream Logic: Synthesis beyond the Bools
Reactive systems that operate in environments with complex data, such as
mobile apps or embedded controllers with many sensors, are difficult to
synthesize. Synthesis tools usually fail for such systems because the state
space resulting from the discretization of the data is too large. We introduce
TSL, a new temporal logic that separates control and data. We provide a
CEGAR-based synthesis approach for the construction of implementations that are
guaranteed to satisfy a TSL specification for all possible instantiations of
the data processing functions. TSL provides an attractive trade-off for
synthesis. On the one hand, synthesis from TSL, unlike synthesis from standard
temporal logics, is undecidable in general. On the other hand, however,
synthesis from TSL is scalable, because it is independent of the complexity of
the handled data. Among other benchmarks, we have successfully synthesized a
music player Android app and a controller for an autonomous vehicle in the Open
Race Car Simulator (TORCS.
- ā¦