Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

BackgroundInterphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata.ResultsHere we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1.ConclusionsWe show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0661-x) contains supplementary material, which is available to authorized users.     

Auxin signaling and transport promote susceptibility to the root-infecting fungal pathogen Fusarium oxysporum in Arabidopsis

Fusarium oxysporum is a root-infecting fungal pathogen that causes wilt disease on a broad range of plant species, including the model plant Arabidopsis thaliana. Currently, very little is known about the molecular or physiological processes that are activated in the host during infection and the roles these processes play in resistance and susceptibility to F. oxysporum. In this study, we analyzed global gene expression profiles of F. oxysporum-infected Arabidopsis plants. Genes involved in jasmonate biosynthesis as well as jasmonate-dependent defense were coordinately induced by F. oxysporum. Similarly, tryptophan pathway genes, including those involved in both indole-glucosinolate and auxin biosynthesis, were upregulated in both the leaves and the roots of inoculated plants. Analysis of plants expressing the DR5:GUS construct suggested that root auxin homeostasis was altered during F. oxysporum infection. However, Arabidopsis mutants with altered auxin and tryptophan-derived metabolites such as indole-glucosinolates and camalexin did not show an altered resistance to this pathogen. In contrast, several auxin-signaling mutants were more resistant to F. oxysporum. Chemical or genetic alteration of polar auxin transport also conferred increased pathogen resistance. Our results suggest that, similarly to many other pathogenic and nonpathogenic or beneficial soil organisms, F. oxysporum requires components of auxin signaling and transport to colonize the plant more effectively. Potential mechanisms of auxin signaling and transport-mediated F. oxysporum susceptibility are discussed.     

A refined synthesis of enantiomerically pure 2-aminocyclobutanecarboxylic acids

The synthesis of enantiomerically pure 2-aminocyclobutanecarboxylic acids has been refined to improve both the efficiency and the simplicity. These improvements provide a shorter and easier access to the racemic cis-cyclobutane β-amino acid core. Derivatization of this material with a chiral non-racemic oxazolidin-2-one allows easy diastereoisomeric separation and presents the advantage of allowing the non-destructive cleavage of the chiral auxiliary either by hydrolysis or by ammonolysis, thus providing an efficacious access to N-protected derivatives of all four stereoisomers of Boc-2-aminocyclobutanecarboxylic acid.     

白马雪山国家级自然保护区典型森林生态系统服务

生态系统服务是近年来生态学研究的热点领域,对关键区域生态系统服务的研究具有重要意义.云南省白马雪山国家级自然保护区地处青藏高原南延部分,拥有独特的地理位置,是生物多样性保护的热点区域.本文对该保护区森林生态系统的生物量与生产力、水源涵养、营养物质循环等3项服务的功能量进行了评估.结果表明:保护区森林总生物量2215.86×104t,生产力171.84×104t·a-1;水源涵养量11964.56×104m3;N、P、K年吸收量分别为26025.94t、2638.57t、12016.85 t.研究表明,保护区森林生态效益显著,对于维持当地以及周边地区的生态安全具有重要意义.     

14-3-3 proteins in neurodegeneration

Among the first reported functions of 14-3-3 proteins was the regulation of tyrosine hydroxylase (TH) activity suggesting a possible involvement of 14-3-3 proteins in Parkinson's disease. Since then the relevance of 14-3-3 proteins in the pathogenesis of chronic as well as acute neurodegenerative diseases, including Alzheimer's disease, polyglutamine diseases, amyotrophic lateral sclerosis and stroke has been recognized. The reported function of 14-3-3 proteins in this context are as diverse as the mechanism involved in neurodegeneration, reaching from basal cellular processes like apoptosis, over involvement in features common to many neurodegenerative diseases, like protein stabilization and aggregation, to very specific processes responsible for the selective vulnerability of cellular populations in single neurodegenerative diseases.Here, we review what is currently known of the function of 14-3-3 proteins in nervous tissue focussing on the properties of 14-3-3 proteins important in neurodegenerative disease pathogenesis.     

Strong spatial genetic structure in peripheral but not core populations of Sitka spruce [Picea sitchensis (Bong.) Carr.

We examined spatial genetic structure within eight populations of Sitka spruce classified as core or peripheral based on ecological niche, and continuous or disjunct based on species distribution. In each population, 200 trees were spatially mapped and genotyped for eight cDNA-based sequence tagged site (STS) codominant markers. Spatial autocorrelation was assessed by estimating p(ij), the average co-ancestry coefficient, between individuals within distance intervals. The distribution of alleles and genotypes within core populations was almost random, with nonsignificant co-ancestry values among trees as close as 50 m in core populations. In contrast, the distribution of alleles and genotypes within peripheral populations revealed an aggregation of similar multilocus genotypes, with co-ancestry values greater than 0.20 among trees up to 50 m apart and significant, positive values between trees up to 500 m. The relatively high density of reproductive adults in core populations may lead to highly overlapping seed shadows that limit development of spatial genetic structure. However, in peripheral populations with a lower density of adults, the distribution of alleles and genotypes was highly structured, likely due to offspring establishment near maternal trees and subsequent biparental inbreeding, as well as more recent population establishment at the leading edge of post-Pleistocene range expansion. Conserving genetic diversity in peripheral populations may require larger reserves for in situ conservation than required in core populations. These data on spatial genetic structure can be used to provide guidance for sampling strategies for both ex situ conservation and research collections.     

The aggregation potential of human amylin determines its cytotoxicity towards islet beta-cells

Human amylin is a small fibrillogenic protein that is the major constituent of pancreatic islet amyloid, which occurs in most subjects with type 2 diabetes. There is evidence that it can elicit in vitro apoptosis in islet beta-cells, but the physical properties that underpin its cytotoxicity have not been clearly elucidated. Here we employed electron microscopy, thioflavin T fluorescence and CD spectroscopy to analyze amylin preparations whose cytotoxic potential was established by live-dead assay in cultured beta-cells. Highly toxic amylin contained few preformed fibrils and initially showed little beta-sheet content, but underwent marked time-dependent aggregation and beta-conformer formation following dissolution. By contrast, low-toxicity amylin contained abundant preformed fibrils, and demonstrated high initial beta-sheet content but little propensity to aggregate further once dissolved. Thus, mature amylin fibrils are not toxic to beta-cells, and aggregates of fibrils such as occur in pancreatic islet amyloid in vivo are unlikely to contribute to beta-cell loss. Rather, the toxic molecular species is likely to comprise soluble oligomers with significant beta-sheet content. Attempts to find ways of protecting beta-cells from amylin-mediated death might profitably focus on preventing the conformational change from random coil to beta-sheet.     

The effect of oxygen on chemotaxis to naphthalene by Pseudomonas putida G7

Chemotactic bacteria can be attracted to electron donors they consume. In systems where donor is heterogeneously distributed, chemotaxis can lead to enhanced removal of donor relative to that achieved in the absence of chemotaxis. However, simultaneous consumption of an electron acceptor may result in the formation of an acceptor gradient to which the bacteria also respond, thus diminishing the positive effect of chemotaxis. Depletion of an electron acceptor can also reduce the rate of electron donor consumption in addition to its effect on chemotaxis. In this study, we examined the effect of oxygen on chemotaxis to naphthalene and on naphthalene consumption by Pseudomonas putida G7. The organism was able to move up an oxygen gradient when there was a naphthalene gradient in the opposite direction. In the absence of an oxygen gradient, low levels of oxygen attenuated chemotaxis to naphthalene but did not affect random motility. The rate of naphthalene consumption decreased at dissolved oxygen concentrations similar to those at which chemotaxis was attenuated. These results suggest that low dissolved oxygen concentrations can reduce naphthalene removal by P. putida G7 in systems where naphthalene is heterogeneously distributed by simultaneously attenuating chemotactic motion toward naphthalene and decreasing the rate of naphthalene degradation.     

Investigations into the mechanisms controlling prostaglandin production by the guinea-pig placenta: roles of calcium and gonadotrophin-releasing hormone

The outputs of PGF(2 alpha), PGE(2) and 6-keto-PGF(1 alpha) were higher from the day 29 guinea-pig placenta than from the sub-placenta in culture, with PGF(2 alpha)being the major prostaglandin produced by the placenta. Lack of extracellular calcium reduced the production of all three prostaglandins by the sub-placenta and 6-keto-PGF(1 alpha) production by the placenta, but had no effect on the production of PGF(2 alpha) and PGE(2) by the placenta. EGTA (a calcium chelator) and a low concentration (30 microM) of TMB-8 (an intracellular calcium antagonist) generally inhibited prostaglandin output from the placenta and sub-placenta at various time points during culture, although EGTA had no effect on PGE(2) output from the placenta. Trifluoperazine and W-7 (calmodulin inhibitors) had no inhibitory effect on the outputs of PGF(2 alpha) and PGE(2) from the placenta, nor on the outputs of any prostaglandin from the sub-placenta. However, these two compounds inhibited the output of 6-keto-PGF(1 alpha) from the placenta. Nifedipine and verapamil (calcium channel blocking drugs) generally reduced the outputs of prostaglandins from the placenta and sub-placenta, except verapamil had no inhibitory effect on PGF(2 alpha) output from the sub-placenta. Gonadotrophin-releasing hormone (GnRH) did not stimulate the output of prostaglandins from the placenta, and tended to have a weak inhibitory action on this tissue. On the sub-placenta, GnRH had an initial inhibitory action on the outputs of PGF(2alpha) and 6-keto-PGF(1 alpha), which was then followed by a stimulation of the outputs of PGF(2 alpha) and, to a lesser extent, of PGE(2).     

Experimental test of nest-site limitation in mature mixed forests of central British Columbia,Canada

Nest-site availability limits cavity-using populations in many harvested forests; however, little is known about the extent of nest-site limitation in mature forests with a full complement of excavator species and intact processes of cavity creation and loss. To examine the role of nest-site availability in limiting cavity-using populations in mature mixed conifer forests in central British Columbia, Canada, we conducted an 11-year before-after control-impact experiment in which we increased nest-site availability via nest box addition. Our 7 sites (3 treatments, 4 controls) had low cavity densities (<2/ha) prior to treatment and cavity occupation rates were also low (<10%/yr), which is a relationship often cited in the literature as evidence of non-limitation in cavity-nesting populations. Following nest box addition at our treatment sites, which tripled the availability of cavities, total density of bird and mammal nests more than tripled. Density of mountain chickadee (Poecile gambeli) nests increased 9-fold on treatment sites and returned to pre-treatment levels following box removal, suggesting that chickadee populations were limited by cavity availability at our study sites. Density of red squirrel (Tamiasciurus hudsonicus) and northern flying squirrel (Glaucomys sabrinus) nests and roosts also increased significantly at treatment sites following box addition and declined following box removal. We noted little change in chickadee or squirrel nest density at control sites monitored concurrently. Squirrels preferred large-sized over small-sized boxes, and significantly enlarged the entrance areas of small boxes by chewing, suggesting that there may have been a shortage of suitable nest and roost sites for them in our study area. We contend that low cavity occupancy rates may not accurately reflect nest-site availability for cavity nesters in mature forests, and that cavity size may influence the true availability of cavities on the landscape. © 2011 The Wildlife Society.