Detection of gene loops by 3C in yeast

“Chromosome conformation capture” (3C) is a powerful method to detect physical interaction between any two genomic loci. 3C involves formaldehyde crosslinking to stabilize transient interactions, followed by restriction digestion, ligation and locus-specific PCR. Accordingly, 3C reveals complex three-dimensional interactions between distal genetic elements within intact cells at high resolution. Here, we describe a modified 3C protocol designed for detection of transient chromatin interactions in the yeast Saccharomyces cerevisiae. Using this protocol, we are able to detect juxtaposition of promoter and terminator regions of genes with ORFs as short as 1 kb in length. We anticipate that this method will be generally applicable to detect dynamic, short-range chromatin interactions and will facilitate the characterization of gene loops and their functional consequences.     

Selectivity of juxtaposition between cup-shaped lactotrophs and gonadotrophs from rat anterior pituitary in culture

Summary Semi-thin sections of three-dimensional reaggregates from adult female rat pituitary, cultured in serum-free defined medium, were stained for prolactin, gonadotropin, thyrotropin, growth hormone and S-100, using the double immunolabelling technique. The frequency of juxtaposition between lactotrophs and gonadotrophs was enumerated and compared with the expected frequency at random distribution of polygonal cell profiles in a hexagonal configuration. The proportions of lactotrophs and gonadotrophs in the aggregate sections were determined using stereometrical analysis. The observed frequency of juxtaposition did not differ significantly from the expected frequency. Hence, no reason was found to assume a selective adhesion between lactotrophs and gonadotrophs in adult female rat pituitary reaggregates. A constant proportion of lactotrophs was found to meet the criteria of a cup-shaped morphology, and 70%±9% (mean ±S.D.) of these so-called cupshaped lactotrophs were found to be juxtaposed at their concave side to gonadotrophs. Administration of 0.01 nM 17-oestradiol to the culture medium resulted in a significant reduction of the proportion of cup-shaped lactotrophs but did not affect the selectivity of juxtaposition to gonadotrophs. The selectivity of juxtaposition between cup-shaped lactotrophs and gonadotrophs may be the morphological correlate of the functional relationship between these cells, which are known to be involved in an intra-pituitary paracrine communication system.     

Bioelectric potential gradients may initiate cell cycling: ELF and zeta potential gradients may mimic this effect

When a number of experimental studies in bioelectromagnetics were reviewed, those in which weak, exogenous extremely low frequency (ELF) fields were applied in fixed juxtaposition to their target tissues, were found to initiate mitogenesis or mitogenesis-related signals more successfully than when the target tissue moved freely during the irradiation. It is suggested that ELF fields in fixed juxtaposition to their target tissue and implanted foreign bodies or endogenous tissues with a significant zeta potential, mimic bioelectric fields generated at wounds. When the potential is high enough, they assist healing by moving cells into the wound and stimulating quiescent cells at the wound margin to cycle. Electrophoresis may help the initial migration of cells into the wound to form a clot, and migration of fibroblasts and epithelial cells from the wound margin. When exposed for a long time in a fixed juxtaposition to a potential gradient too weak to show in situ microelectrophoresis along the cell membrane surface, surface particles may coalesce to form microclusters, where like-charged surface particles are in close proximity, and growth factor receptor oligomerization and other cycle-initiating reactions are facilitated. Bioelectromagnetics 18:341–348, 1997. © 1997 Wiley-Liss, Inc.     

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites.

There are many proteins that interact simultaneously with two or more DNA sites that are separated along the DNA contour. These sites must be brought close together to form productive complexes with the proteins. We used Monte Carlo simulation of supercoiled DNA conformations to study the effect of supercoiling and DNA length on the juxtaposition of DNA sites, the angle between them, and the branching of the interwound superhelix. Branching decreases the probability of juxtaposition of two DNA sites but increases the probability of juxtaposition of three sites at branch points. We found that the number of superhelix branches increases linearly with the length of DNA from 3 to 20 kb. The simulations showed that for all contour distances between two sites, the juxtaposition probability in supercoiled DNA is two orders of magnitude higher than in relaxed DNA. Supercoiling also results in a strong asymmetry of the angular distribution of juxtaposed sites. The effect of supercoiling on site-specific recombination and the introduction of supercoils by DNA gyrase is discussed in the context of the simulation results.     

The balancing of virtues—Muslim perspectives on palliative and end of life care: Empirical research analysing the perspectives of service users and providers

In this paper, I will share findings from a qualitative study that offers a thematic analysis of 76 interviews with Muslim patients and families as well as doctors, nurses, allied health professionals, chaplains and community faith leaders across the United Kingdom. The data show that for many Muslims, Islam—its texts and lived practice—is of central importance when they are deliberating about death and dying . Central to these deliberations are virtues rooted within Islamic theology and ethics, the traditions of adab (virtue) and aqhlaq (proper conduct). Themes analysed include theological and moral understandings around the virtues of hope and acceptance. The study provides an analysis of these themes in relation to the experiences of Muslim patients and families arriving at meaning making around death and dying and how this interfaces with their interaction with biomedicine and healthcare. The study shows that the juxtaposition of different values and moral frameworks require careful negotiation when Muslim patients and families encounter the healthcare system. The study also describes how healthcare professionals and staff of other faiths and no faith encounter Muslim beliefs and practices, and the challenges they face in interpreting virtues and values rooted in faith, especially when these are perceived to be mutually opposed or inconsistent.     

In VitroAssays for Activities of Retroviral Integrase

Integration of retroviral DNA, an essential step during the retroviral life cycle, is mediated by the viral protein integrase. Simplein vitroassays for measuring integrase activities are described, including catalysis (3′-end processing, 3′-end joining, disintegration), juxtaposition of viral DNA ends, DNA binding, and target site selection. The described assays will be useful in elucidating the molecular mechanism of retroviral integration and screening for integrase inhibitors as potential anti-retroviral drugs.     

An estimation of the dimensions of the phycocyanin molecule

Knowledge of the total particle volume and the specific volumes of the constituent polar and nonpolar amino acid residues of a globular protein may be used in suitable instances to estimate the size and shape, of the macromolecule. Use has been made of the data, which is available in the literature for phycocyanin from Plectonema calothricoidcs, to predict possible models for the monomer and hexamer forms of this protein. The monomer is well represented by a prolate ellipsoid with semiaxes of 45 and 17Å and an approximate molecular weight of (46000). The hexamer is envisaged as the aggregate of six such monomers, in juxtaposition, with their major axes parallel so as to form a closed ring structure of about 268000 molecular weight. These proposed models are consistent with the previously published electron micrographs and hydrodynamic properties of this protein.     

Freeze-fracture study of the chromaffin cell during exocytosis: Evidence for connections between the plasma membrane and secretory granules and for movements of plasma membrane-associated particles

Summary Exocytosis was studied in acetylcholine-stimulated bovine adrenal medulla. During a pre-exocytotic stage, chromaffin granules are found in juxtaposition to the plasma membrane and separated from it by an electron dense space 25–27 Å in width. Freeze-fracture studies show this stage to be characterized by connections between the granules and the plasma membrane. These connections are apparently cytoplasmic but bridge both membranes; they are presumably proteinaceous, but their exact nature remains to be elucidated. Later stages of exocytosis were also studied by the freeze-fracture technique; a typical feature is the lack of intramembrane particles around the fusion site. Both connections and membrane particle movement are discussed in terms of recent biochemical findings.     

A Delta-Notch signaling border regulated by Engrailed/Invected repression specifies boundary cells in the Drosophila hindgut

The Drosophila hindgut develops three morphologically distinct regions along its anteroposterior axis: small intestine, large intestine and rectum. Single-cell rings of 'boundary cells' delimit the large intestine from the small intestine at the anterior, and the rectum at the posterior. The large intestine also forms distinct dorsal and ventral regions; these are separated by two single-cell rows of boundary cells. Boundary cells are distinguished by their elongated morphology, high level of both apical and cytoplasmic Crb protein, and gene expression program. During embryogenesis, the boundary cell rows arise at the juxtaposition of a domain of Engrailed (En)- plus Invected (Inv)-expressing cells with a domain of Delta (Dl)-expressing cells. Analysis of loss-of-function and ectopic expression phenotypes shows that the domain of Dl-expressing cells is defined by En/Inv repression. Further, Notch pathway signaling, specifically the juxtaposition of Dl-expressing and Dl-non-expressing cells, is required to specify the rows of boundary cells. This Notch-induced cell specification is distinguished by the fact that it does not appear to utilize the ligand Serrate and the modulator Fringe.     

Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases

The mathematical basis of the hypothesis that type-2 topoisomerases recognize and act at specific DNA juxtapositions has been investigated by coarse-grained lattice polymer models, showing that selective segment passages at hooked juxtapositions can result in dramatic reductions in catenane and knot populations. The lattice modeling approach is here extended to account for the narrowing of variance of linking number (Lk) of DNA circles by type-2 topoisomerases. In general, the steady-state variance of Lk resulting from selective segment passages at a specific juxtaposition geometry j is inversely proportional to the average linking number, 〈Lk〉_j, of circles with the given juxtaposition. Based on this formulation, we demonstrate that selective segment passages at hooked juxtapositions reduce the variance of Lk. The dependence of this effect on model DNA circle size is remarkably similar to that observed experimentally for type-2 topoisomerases, which appear to be less capable in narrowing Lk variance for small DNA circles than for larger DNA circles. This behavior is rationalized by a substantial cancellation of writhe in small circles with hook-like juxtapositions. During our simulations, we uncovered a twisted variation of the hooked juxtaposition that has an even more dramatic effect on Lk variance narrowing than the hooked juxtaposition. For an extended set of juxtapositions, we detected a significant correlation between the Lk narrowing potential and the logarithmic decatenating and unknotting potentials for a given juxtaposition, a trend reminiscent of scaling relations observed with experimental measurements on type-2 topoisomerases from a variety of organisms. The consistent agreement between theory and experiment argues for type-2 topoisomerase action at hooked or twisted-hooked DNA juxtapositions.     

Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action

Lattice modeling is applied to investigate how the configurations of local chain juxtapositions may provide information about whether two ring polymers (loops) are topologically linked globally. Given a particular juxtaposition, the conditional probability that the loops are linked is determined by exact enumeration and extensive Monte Carlo sampling of conformations satisfying excluded volume constraints. A discrimination factor fL, defined as the ratio of linked to unlinked probabilities, varies widely depending on which juxtaposition is presumed. /log fL/s that are large for small loop size n tend to decrease, signaling diminishing topological information content of the juxtapositions, with increasing n. However, some juxtaposition geometries can impose sufficient overall conformational biases such that /log fL/ remains significant for large n. Notably, for two loops as large as n=200 in the model, the probability that passing the segments of a hooked juxtaposition would unlink an originally linked configuration is remarkably high, approximately 85%. In contrast, segment-passage of a free juxtaposition would link the loops from an originally unlinked configuration more than 90% of the time. The statistical mechanical principles emerging from these findings suggest that it is physically possible for DNA topoisomerases to decatenate effectively by acting selectively on juxtapositions with specific "hooked" geometries.     

Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases

Topoisomerases may unknot by recognizing specific DNA juxtapositions. The physical basis of this hypothesis is investigated by considering single-loop conformations in a coarse-grained polymer model. We determine the statistical relationship between the local geometry of a juxtaposition of two chain segments and whether the loop is knotted globally, and ascertain how the knot/unknot topology is altered by a topoisomerase-like segment passage at the juxtaposition. Segment passages at a "free" juxtaposition tend to increase knot probability. In contrast, segment passages at a "hooked" juxtaposition cause more transitions from knot to unknot than vice versa, resulting in a steady-state knot probability far lower than that at topological equilibrium. The reduction in knot population by passing chain segments through a hooked juxtaposition is more prominent for loops of smaller sizes, n, but remains significant even for larger loops: steady-state knot probability is only approximately 2%, and approximately 5% of equilibrium, respectively, for n=100 and 500 in the model. An exhaustive analysis of approximately 6000 different juxtaposition geometries indicates that the ability of a segment passage to unknot correlates strongly with the juxtaposition's "hookedness". Remarkably, and consistent with experiments on type-2 topoisomerases from different organisms, the unknotting potential of a juxtaposition geometry in our polymer model correlates almost perfectly with its corresponding decatenation potential. These quantitative findings suggest that it is possible for topoisomerases to disentangle by acting selectively on juxtapositions with "hooked" geometries.     

How landscape scale changes affect ecological processes in conservation areas: external factors influence land use by zebra (Equus burchelli) in the Okavango Delta

Most large‐bodied wildlife populations in sub‐Saharan Africa only survive in conservation areas, but are continuing to decline because external changes influence ecological processes within reserves, leading to a lack of functionality. However, failure to understand how landscape scale changes influence ecological processes limits our ability to manage protected areas. We used GPS movement data to calculate dry season home ranges for 14 zebra mares in the Okavango Delta and investigated the effects of a range of landscape characteristics (number of habitat patches, mean patch shape, mean index of juxtaposition, and interspersion) on home range size. Resource utilization functions (RUF) were calculated to investigate how specific landscape characteristics affected space use. Space use by all zebra was clustered. In the wetter (Central) parts of the Delta home range size was negatively correlated with the density of habitat patches, more complex patch shapes, low juxtaposition of habitats and an increased availability of floodplain and grassland habitats. In the drier (Peripheral) parts of the Delta, higher use by zebra was also associated with a greater availability of floodplain and grassland habitats, but a lower density of patches and simpler patch shapes. The most important landscape characteristic was not consistent between zebra within the same area of the Delta, suggesting that no single foraging strategy is substantially superior to others, and so animals using different foraging strategies may all thrive. The distribution and complexity of habitat patches are crucial in determining space use by zebra. The extent and duration of seasonal flooding is the principal process affecting habitat patch characteristics in the Okavango Delta, particularly the availability of floodplains, which are the habitat at greatest risk from climate change and anthropogenic disturbance to the Okavango's catchment basin. Understanding how the factors that determine habitat complexity may change in the future is critical to the conservation of large mammal populations. Our study shows the importance of maintaining flood levels in the Okavango Delta and how the loss of seasonal floodplains will be compounded by changes in habitat configuration, forcing zebra to change their relative space use and enlarge home ranges, leading to increased competition for key resources and population declines.     

The trace metal economy of the coral holobiont: supplies,demands and exchanges

The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.     

Phenotypic heterogeneity in three cases of lymphoid malignancy with chromosomal translocations in 14q11

Lymphoid malignancies bearing translocations involving the region 14q11 are thought to have a T-cell phenotype because their pathogenesis is postulated to involve the aberrant juxtaposition of DNA sequences active in T-cell differentiation (T-cell antigen receptor genes) and proto-oncogenes. We present here three lymphoid malignancies with translocations involving 14q11. Although one had a T-cell phenotype, the other two had B-cell lineage phenotypes. Our findings confirm that not all lymphoid malignancies with translocations involving 14q11 represent T-cell clonal expansions.     

The adenylyl and guanylyl cyclase superfamily

New structures solved in 1997 revealed that the adenylyl cyclase core consists of a pair of catalytic domains arranged in a wreath. Homologous catalytic domains are arranged in diverse adenylyl and guanylyl cyclases as symmetric homodimers or pseudosymmetric heterodimers. The kinship of the adenylyl and guanylyl cyclases has been confirmed by the structure-based interconversion of their nucleotide specificities. Catalysis is activated when two metal-binding aspartate residues on one domain are juxtaposed with a key aspargine—arginine pair on the other. Allosteric activators of mammalian adenylyl cyclase, forskolin and the stimulatory G protein α subunit, promote the catalytically optimal juxtaposition of the two domains.     

Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA

Eukaryotic topoisomerases I and II efficiently remove helical tension in naked DNA molecules. However, this activity has not been examined in nucleosomal DNA, their natural substrate. Here, we obtained yeast minichromosomes holding DNA under (+) helical tension, and incubated them with topoisomerases. We show that DNA supercoiling density can rise above +0.04 without displacement of the histones and that the typical nucleosome topology is restored upon DNA relaxation. However, in contrast to what is observed in naked DNA, topoisomerase II relaxes nucleosomal DNA much faster than topoisomerase I. The same effect occurs in cell extracts containing physiological dosages of topoisomeraseI and II. Apparently, the DNA strand-rotation mechanism of topoisomerase I does not efficiently relax chromatin, which imposes barriers for DNA twist diffusion. Conversely, the DNA cross-inversion mechanism of topoisomerase II is facilitated in chromatin, which favor the juxtaposition of DNA segments. We conclude that topoisomerase II is the main modulator of DNA topology in chromatin fibers. The nonessential topoisomerase I then assists DNA relaxation where chromatin structure impairs DNA juxtaposition but allows twist diffusion.