Damage site chromatin: open or closed?

Technical advances in recent years, such as laser microirradiation and chromatin immunoprecipitation, have led to further understanding of DNA damage responses and repair processes as they happen in vivo and have allowed us to better evaluate the activities of new factors at damage sites. Facilitated by these tools, recent studies identified the unexpected roles of heterochromatin factors in DNA damage recognition and repair, which also involves poly(ADP-ribose) polymerases (PARPs). The results suggest that chromatin at damage sites may be quite structurally dynamic during the repair process, with transient intervals of 'closed' configurations before a more 'open' arrangement that allows the repair machinery to access damaged DNA.     

Membrane geometry of “open” prolamellar bodies

Summary The open type of prolamellar body in etiplasts was examined by electron microscopy to characterise its three-dimensional organisation. As in more compact forms of prolamellar body, its basic geometric unit is a tetrahedrally branched tubule. In the open type, these lie smoothly confluent with one another at the vertices of 5- and 6-membered rings which circumscribe the faces of three kinds of polyhedra: pentagonal dodecahedra (with 12 pentagonal faces), 14-hedra (2 opposite hexagonal faces joined by two circlets of six pentagonal faces), and 15-hedra (3 hexagonal and 12 pentagonal faces). These polyhedra join confluently in their turn, sharing faces with one another in at least one recognisable superstructure which accounts for the appearance of open prolamellar bodies in many ultrathin sections. In this organisation, columns of pentagonal dodecahedra are arranged at 120 ° to one another in the x-y-plane of the lattice. They do not fill the plane but intersect so as to delimit voids in the form of hexagonally arranged 14-hedra (with hexagonal rings in the x-y-plane). Strata of this type alternate with strata made of face-sharing 15-hedra (with their hexagonal rings normal to x-y), which also delimit 14-hedra. The 14-hedra thus lie in register in the z-axis in hexagonally arranged columns, normal to the alternating strata. Other possible organisations cannot be excluded and local variations and dislocations certainly occur, but many micrographs that display elements of symmetry in open prolamellar bodies can be matched to thin slices through such a model. Its geometry is like that of the cages of water molecules in type IV (sensu Jeffrey=type IIIsensu O'Keeffe) clathrate-hydrates, point group P6/mmm, but about two orders of magnitude larger.     

Sliding clamps: an open and shut case?

Molecular events in the clamp-loading reaction pathway of DNA replication are revealed by new crystal structures of bacteriophage T4 clamp loader-clamp-DNA complexes that capture two distinct conformations with the clamp open and closed.     

Is microclimate important for Orthoptera in open landscapes?

Orthoptera were monitored on field edge public footpaths on the east (leeward) and west (windward) side of hedgerows in Chelmsford, UK, in 2006. A total of 6 species were recorded from footpaths on the leeward side of hedgerows probably due to the shelter from the prevailing westerly winds provided by the trees and shrubs. On the windward side of hedgerows species richness and abundance of Orthoptera were reduced (only 4 species were recorded). It is suggested that shelter from the wind and the exposure to early morning sunlight for Orthoptera on the east side of hedgerows are important factors governing their occurrence on farmland. Many replicates had Environmental Stewardship (ES) scheme field margins adjacent but they did not affect Orthoptera species richness or abundance.     

OECD guidelines on open access: commercialization in disguise?

The Organisation for Economic Co-operation and Development (OECD) has published a new set of principles and guidelines to promote open access to datasets and results from publicly funded research. However, there is reason to think twice about the implications of making demands for transparency and open access for publicly funded research only. How will such demands affect incentives and research agendas? Might this new regulation of publicly funded research have undesirable effects on the quality and value of research? Placing the OECD guidelines in a broader context of research regulation, we argue that they might provide a further push toward collaboration with commercially sponsored research and reinforce incentive structures that favour the creation of commercial value.     

How fast does the GluR1Qflip channel open?

Opening of a ligand-gated ion channel is the step at which the binding of a neurotransmitter is transduced into the electrical signal by allowing ions to flow through the transmembrane channel, thereby altering the postsynaptic membrane potential. We report the kinetics for the opening of the GluR1Qflip channel, an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit of the ionotropic glutamate receptors. Using a laser-pulse photolysis technique that permits glutamate to be liberated photolytically from gamma-O-(alpha-carboxy-2-nitrobenzyl)glutamate (caged glutamate) with a time constant of approximately 30 micros, we show that, after the binding of glutamate, the channel opened with a rate constant of (2.9 +/- 0.2) x 10(4) s(-1) and closed with a rate constant of (2.1 +/- 0.1) x 10(3) s(-1). The observed shortest rise time (20-80% of the receptor current response), i.e. the fastest time by which the GluR1Qflip channel can open, was predicted to be 35 micros. This value is three times shorter than those previously reported. The minimal kinetic mechanism for channel opening consists of binding of two glutamate molecules, with the channel-opening probability being 0.93 +/- 0.10. These findings identify GluR1Qflip as one of the temporally efficient receptors that transduce the binding of chemical signals (i.e. glutamate) into an electrical impulse.     

Activation of PKR: an open and shut case?

The double-stranded (ds) RNA-activated protein kinase, PKR, has a key role in the innate immunity response to viral infection in higher eukaryotes. PKR contains an N-terminal dsRNA-binding domain and a C-terminal kinase domain. In the prevalent autoinhibition model for PKR activation, dsRNA binding induces a conformational change that leads to the release of the dsRNA-binding domain from the kinase, thus relieving the inhibition of the latent enzyme. Structural and biophysical data now favor a model whereby dsRNA principally functions to induce dimerization of PKR via the kinase domain. This dimerization model has implications for other PKR regulatory mechanisms and represents a new structural paradigm for control of protein kinase activity.     

Mind the gap: how open were European primeval forests?

There are two competing hypotheses about the structure and dynamics of primeval forests in lowland Europe: the high-forest and the wood-pasture hypotheses, both of which influence current European forest conservation policies. In a recent study using pollen-analytical data from across lowland Europe, Mitchell provides support for rejecting the wood-pasture hypothesis. His study is important for future forest management planning and for showing how hypotheses about large herbivores as biotic factors can be tested using palaeoecological data.     

Microtubule motors and pollen tube growth—still an open question

The growth of pollen tubes is supported by the continuous supply of secretory vesicles in the tip area. Movement and accumulation of vesicles is driven by the dynamic interplay between the actin cytoskeleton and motor proteins of the myosin family. A combination of the two protein systems is also responsible for the bidirectional movement of larger organelle classes. In contrast, the role of microtubules and microtubule-based motors is less clear and often ambiguous. Nevertheless, there is evidence which shows that the pollen tube contains a number of microtubule-based motors of the kinesin family. These motor proteins are likely to be associated with pollen tube organelles and, consequently, they have been hypothesized to participate in the distribution of organelles during pollen tube growth. Whether microtubule motor proteins take part in either the transport or positioning of organelles is not known for sure, but there is evidence for this second possibility. This review will discuss the current knowledge of microtubule-based motor proteins (including kinesins and hypothetical dyneins) and will make some hypothesis about their role in the pollen tube.     

Nitrogen fixation and transfer in open ocean diatom–cyanobacterial symbioses

Many diatoms that inhabit low-nutrient waters of the open ocean live in close association with cyanobacteria. Some of these associations are believed to be mutualistic, where N₂-fixing cyanobacterial symbionts provide N for the diatoms. Rates of N₂ fixation by symbiotic cyanobacteria and the N transfer to their diatom partners were measured using a high-resolution nanometer scale secondary ion mass spectrometry approach in natural populations. Cell-specific rates of N₂ fixation (1.15–71.5 fmol N per cell h⁻¹) were similar amongst the symbioses and rapid transfer (within 30 min) of fixed N was also measured. Similar growth rates for the diatoms and their symbionts were determined and the symbiotic growth rates were higher than those estimated for free-living cells. The N₂ fixation rates estimated for Richelia and Calothrix symbionts were 171–420 times higher when the cells were symbiotic compared with the rates estimated for the cells living freely. When combined, the latter two results suggest that the diatom partners influence the growth and metabolism of their cyanobacterial symbionts. We estimated that Richelia fix 81–744% more N than needed for their own growth and up to 97.3% of the fixed N is transferred to the diatom partners. This study provides new information on the mechanisms controlling N input into the open ocean by symbiotic microorganisms, which are widespread and important for oceanic primary production. Further, this is the first demonstration of N transfer from an N₂ fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems.     

Does MAX open up a new avenue for meiotic research?

Meiosis is a central event of sexual reproduction. Like somatic cells, germ cells conduct mitosis to increase their cell number, but unlike somatic cells, germ cells switch their cell division mode from mitosis to meiosis at a certain point in gametogenesis. However, the molecular basis of this switch remains elusive. In this review article, we give an overview of the onset of mammalian meiosis, including our recent finding that MYC Associated Factor X (MAX) prevents ectopic and precocious meiosis in embryonic stem cells (ESCs) and germ cells, respectively. We present a hypothetical model of a MAX‐centered molecular network that regulates meiotic entry in mammals and propose that inducible Max knockout ESCs provide an excellent platform for exploring the molecular mechanisms of meiosis initiation, while excluding other aspects of gametogenesis.     

Mucosal junctions: open doors to HPV and HIV infections?

Throughout adult life, new developmental commitment of adult stem cells causes reversible epithelial replacements in various mucosal surfaces, including the uterine cervix and the anal canal. Located at the squamocolumnar junctions, these metaplastic conversions are associated with chronic inflammation and deregulated expression of soluble and cell-membrane factors important for antiviral immune response. In this paper, we propose that these histological and immunological features increase the susceptibility of these metaplastic microenvironments to human papillomavirus and human immunodeficiency virus infections. Identification of the anatomical sites and cell populations within the anogenital tract, which is the site primary infected by these viruses, is crucial for the understanding of the pathogenesis of viral disease and development of antiviral strategies.     

Potential open reading frames in 5′-untranslated regions of eukaryotic mRNA

It is known that 5′-untranslated sequences of eukaryotic mRNA often contain AUG triplets, which can serve as translation initiation sites. It is assumed that such leader open reading frames can perform regulatory functions and code functionally active proteins; however, their characteristics have been studied insufficiently. In the article, the context organization of leader open reading frames of eukaryotic mRNA was considered. It was shown that their characteristics correlate with their position with respect to the protein-coding sequence, which may be related to the translation initiation efficiency.