Evolution of the regular zone of histone H1 in Fabaceae plants

An analysis of the historic H1 subtype, H1-1, in eight legumes belonging to four genera of the tribe Vicieae (Pisum, Lathyrus, Lens, and Vicia), revealed an extended region consisting of the tandemly repeated AKPAAK motifs. We named this region the Regular zone (RZ). The AKPAAK motifs are organized into two blocks separated by a short (two or six amino acids) intervening sequence (IS). The distal block contains six AKPAAK motifs, while the number of repeats in the proximal block varies from six in V. faba to seven in the other species. In V. hirsuta, the first two repeated units of the proximal block are octapeptides AKAKPAAK. The apparent rate of synonymous substitutions in the blocks of RZ is much higher than in the rest of the gene. This can be explained by repeat shuffling within each block. In the C-domain of the orthologous H1 subtype froth Medicago truncatula (tribe Trifolieae), a region corresponding to the RZ of Vicieae species was found. It also consists of two blocks of AKPAAK motifs (four and three repeats in the proximal and distal blocks, respectively). These blocks are separated by a 20-amino acid IS. The first 20 amino acids of the Medicago RZ are not part of AKPAAK repeats. We hypothesise that the RZ has most probably evolved as a result of an expansion of AKPAAK repeats from two separate sites in the C-domain. This process started tens of millions of years ago and was most likely directed by positive selection.

Symmetry contaminations in reactive scattering through long-lived collision complexes

We extend our Lanczos subspace time-independent wave packet method [J. Chem. Phys. 116 (2002) 2354] to investigate the issue of symmetry contaminations for the challenging deep-well H + O-2 reaction. Our central objective is to address the issue of whether significant symmetry contamination can occur if a wavepacket initially possessing the correct O-O exchange symmetry is propagated over tens of thousands of recursive steps using a basis which does not explicitly enforce the correct symmetry, and if so how seriously this affects the results. We find that symmetry contamination does exist where the symmetry constraint is not explicitly enforced in the basis. While it affects individual resonances and the associated peak amplitudes, the overall shape of the more averaged quantities such as total reaction probabilities and vibrational branching ratios are not seriously affected. (C) 2004 Elsevier B.V. All rights reserved.

ELA-ICP-MS U-Pb zircon geochronology of regional volcanism hosting the Bajo de la Alumbrera Cu-Au deposit: implications for porphyry-related mineralization

ELA-ICP-MS U-Pb zircon geochronology has been used to show that the porphyritic intrusions related to the formation of the Bajo de la Alumbrera porphyry Cu-Au deposit, NW Argentina, are cogenetic with stratigraphically well-constrained volcanic and volcaniclastic rocks of the Late Miocene Farallon Negro Volcanic Complex. Zircon geochronology for intrusions in this deposit and the host volcanic sequence show that multiple mineralized porphyries were emplaced in a volcanic complex that developed over 1.5 million years. Volcanism occurred in a multivent volcanic complex in a siliciclastic intermontane basin. The complex evolved from early mafic-intermediate effusive phases to a later silicic explosive phase associated with mafic intrusions. Zircons from the basal mafic-intermediate lavas have ages that range from 8.46 +/- 0.14 to 7.94 +/- 0.27 Ma. Regionally extensive silicic explosive volcanism occurred at similar to8.0 Ma (8.05 +/- 0.13 and 7.96 +/- 0.11 Ma), which is co-temporal with intrusion of the earliest mineralized porphyries at Bajo de la Alumbrera (8.02 +/- 0.14 and 7.98 +/- 0.14 Ma). Regional uplift and erosion followed during which the magmatic-hydrothermal system was probably unroofed. Shortly thereafter, dacitic lava domes were extruded (7.95 +/- 0.17 Ma) and rhyolitic diatremes (7.79 +/- 0.13 Ma) deposited thick tuff blankets, across the region. Emplacement of large intermediate composition stocks occurred at 7.37 +/- 0.22 Ma, shortly before renewed magmatism occurred at Bajo de la Alumbrera (7.10 +/- 0.07 Ma). The latest porphyry intrusive event is temporally associated with new ore-bearing magmatic-hydrothermal fluids. Other dacitic intrusions are associated with subeconomic deposits that formed synchronously with the mineralized porphyries at Bajo de la Alumbrera. However, their emplacement continued (from 7.10 +/- 0.06 to 6.93 +/- 0.07 Ma) after the final intrusion at Bajo de al Alumbrera. Regional volcanism had ceased by 6.8 Ma (6.92 +/- 0.07 Ma). The brief history of the volcanic complex hosting the Bajo de la Alumbrera Cu-Au deposit differs from that of other Andean provinces hosting porphyry deposits. For example, at the El Salvador porphyry copper district in Chile, magmatism related to Cu mineralization was episodic in regional igneous activity that occurred over tens of millions of years. Bajo de la Alumbrera resulted from the superposition of multiple porphyry-related hydrothermal systems, temporally separated by a million years. It appears that the metal budget in porphyry ore deposits is not simply a function of their longevity and/or the superposition of multiple porphyry systems. Nor is it a function of the duration of the associated cycle of magmatism. Instead, the timing of processes operating in the parental magma body is the controlling factor in the formation of a fertile porphyry-related ore system.

Intertidal habitat conservation: identifying conservation targets in the absence of detailed biological information

1. Growing concern associated with threats to the marine environment has resulted in an increased demand for marine reserves that conserve representative and adequate examples of biodiversity. Often, the decisions about where to locate reserves must be made in the absence of detailed information on the patterns of distribution of the biota. Alternative approaches are required that include defining habitats using surrogates for biodiversity. Surrogate measures of biodiversity enable decisions about where to locate marine reserves to be made more reliably in the absence of detailed data on the distribution of species. 2. Intertidal habitat types derived using physical properties of the shoreline were used as a surrogate for intertidal biodiversity to assist with the identification of sites for inclusion in a candidate system of intertidal marine reserves for 17 463 km of the mainland coast of Queensland, Australia. This represents the first systematic approach, on essentially one-dimensional data, using fine-scale (tens to hundreds of metres) intertidal habitats to identify a system of marine reserves for such a large length of coast. A range of solutions would provide for the protection of a representative example of intertidal habitats in Queensland. 3. The design and planning of marine and terrestrial protected areas systems should not be undertaken independently of each other because it is likely to lead to inadequate representation of intertidal habitats in either system. The development of reserve systems specially designed to protect intertidal habitats should be integrated into the design of terrestrial and marine protected area systems. Copyright (c) 2005 John Wiley & Sons, Ltd.

Effects of harvesting callianassid (ghost) shrimps on subtropical benthic communities

The effects of harvesting of callianassid shrimp (Trypaea australiensis) on the abundance and composition of macrobenthic assemblages in unvegetated sediments of a subtropical coastal embayment in Queensland, Australia were examined using a combination of sampling and manipulative experiments. First, the abundance and composition of the benthic infauna in an area regularly used for the collection of shrimp for bait by recreational anglers was compared with multiple reference areas. Second, a BACI design, with multiple reference areas, was used to examine the short-term effects of harvesting on the benthic assemblages from an intensive commercialised fishing competition. Third, a large-scale, controlled manipulative experiment, where shrimp were harvested from 10,000 m(2) plots at intensities commensurate with those from recreational and commercial operators, was done to determine the impacts on different components of the infaunal assemblage. Only a few benthic taxa showed significant declines in abundance in response to the removal of ghost shrimp from the unvegetated sediments. There was evidence, however, of more subtle effects with changes in the degree of spatial variation (patchiness) of several taxa as a result of harvesting.. Groups such as capitellid polychaetes, gammarid amphipods and some bivalves were significantly more patchy in their distribution in areas subjected to harvesting than reference areas, at a scale of tens of metres. This scale corresponds to the patterns of movement and activity of recreational harvesters working in these areas. In contrast, patchiness in the abundance of ghost shrimp decreased significantly under harvesting at scales of hundreds of metres, in response to harvesters focussing their efforts on areas with greater numbers of burrow entrances, leading to a more even distribution of the animals. Controlled experimental harvesting caused declines in the abundance of soldier crabs (Mictyris longicarpus), polychaetes and amphipods and an increase in the spatial patchiness of polychaetes. Populations of ghost shrimp were, however, resilient to harvesting over extended periods of time. In conclusion, harvesting of ghost shrimp for bait by recreational and commercial fishers causes significant but localised impacts on a limited range of benthic fauna in unvegetated sediments, including changes in the degree of spatial patchiness in their distribution. (c) 2005 Elsevier B.V. All rights reserved.

Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L.

Genetic variation at microsatellite markers was used to quantify genetic structure and mating behavior in a severely fragmented population of the wind-pollinated, wind-dispersed temperate tree Fraxinus excelsior in a deforested catchment in Scotland. Remnants maintain high levels of genetic diversity, comparable with those reported for continuous populations in southeastern Europe, and show low interpopulation differentiation (Theta = 0.080), indicating that historical gene exchange has not been limited (Nm = 3.48). We estimated from seeds collected from all trees producing fruits in three of five remnants that F. excelsior is predominantly outcrossing (t(m). = 0.971 +/- 0.028). Use of a neighborhood model approach to describe the relative contribution of local and long-distance pollen dispersal indicates that pollen gene flow into each of the three remnants is extensive (46-95%) and pollen dispersal has two components. The first is very localized and restricted to tens of meters around the mother trees. The second is a long-distance component with dispersal occurring over several kilometers. Effective dispersal distances, accounting for the distance and directionality to mother trees of sampled pollen donors, average 328 m and are greater than values reported for a continuous population. These results suggest that the opening of the landscape facilitates airborne pollen movement and may alleviate the expected detrimental genetic effects of fragmentation.

Simulated rainwater effects on anion exchange capacity and nitrate retention in Ferrosols

Nitrate (NO3) accumulations (up to 1880 kg NO3-N/ha for a 12-m profile) in the soils of the Johnstone River catchment (JRC) may pose a serious environmental threat to the Great Barrier Reef lagoon if the NO3 were released. The: leaching of artificial rainwater through repacked soil columns was investigated to determine the effect of low NO3/low ionic strength inputs on the NO3 Chemistry of the JRC profiles. Repacked soil columns were used to simulate the 11.5-m profiles, and the soil solution anion and cation concentrations were monitored at 10 points throughout the soil column. As the rainwater was applied, NO3 leached down the profile, with substantial quantities exiting the columns. Anion exchange was discounted as the major mechanism of NO3 release due to the substantial net loss of anions from the system (up to 2740 kg NO3-N/ha over the experimental period). As the soils were dominated by variable charge minerals, the effect of changing pH and ionic strength on the surface charge density was investigated in relation to the release of NO3 from the exchange. It was concluded that the equilibration of the soil solution with the low ionic strength rainwater solution resulted in a lessening of both the positive and negative surface charge. Nitrate was released into the soil solution and subsequently leached due to the lessening of the positive surface charge. Loss of NO3 from the soil profile was slow, with equivalent field release times estimated to be tens of years. Although annual release rates were high in absolute terms (up to 175 kg NO3-N/ha.year), they are only slightly greater than the current loss rates from fertilised sugarcane production (up to 50 kg NO3-N/ha.year). In addition to this, the large-scale release of NO3 from the accumulations will only occur until a new equilibrium is established with the input rainwater solution.

Environmental contamination of arsenic and its toxicological impact on humans

Inorganic arsenic compounds are known carcinogens. The human epidemiologic evidence of arsenic-induced skin, lung, and bladder cancers is strong. However, the evidence of arsenic carcinogenicity in animals is very limited. Lack of a suitable animal model until recent years has inhibited studies of the mechanism of arsenic carcinogenesis. The toxicity and bioavailability of arsenic depend on its solubility and chemical forms. Therefore, it is critical to be able to measure arsenic speciation accurately and reliably. However, speciation of arsenic in more complex matrices remains a real challenge. There are tens of millions of people who are being exposed to excessive levels of arsenic in the drinking water alone. The source of contamination is mainly of natural origin and the mass poisoning is occurring worldwide, particularly in developing countries. Chronic arsenicosis resulting in cancer and non-cancer diseases will impact significantly on the public health systems in their respective countries. Effective watershed management and remediation technologies in addition to medical treatment are urgently needed in order to avoid what has been regarded as the largest calamity of chemical poisoning in the world.

Local therapy for restenosis

The durability of all forms of open or percutaneous revascularisation is affected by the development of localised stenoses within the bypass graft or at the site of endarterectomy, stent or angioplasty. The reported incidence of significant restenosis has varied dependent on initial procedure, site, case mix and definition, but is greatest during the first 12 months (Table 1).1 Over the last 40 years tens of thousands of studies have been carried out in an effort to understand or reduce the incidence of restenosis, with two major mechanisms identified as being responsible for the luminal narrowing, namely intimal hyperplasia and constrictive remodelling. Intimal hyperplasia is provoked by changes in the balance of local cytokines controlling vascular smooth muscle cell (VSMC) proliferation, apoptosis and migration, brought about by endothelial or medial injury and alterations in haemodynamic forces. The overall vessel diameter reduction that occurs in constrictive remodelling is less well defined, but likely involves matrix turnover under the control of proteinases, particularly metalloproteinases.

Swimming against the flow: A mechanism of zooplankton aggregation

Zooplankton reside in a constantly flowing environment. However, information about their response to ambient flow has remained elusive, because of the difficulties of following the individual motions of these minute, nearly transparent animals in the ocean. Using a three-dimensional acoustic imaging system, we tracked >375,000 zooplankters at two coastal sites in the Red Sea. Resolution of their motion from that of the water showed that the animals effectively maintained their depth by swimming against upwelling and downwelling currents moving at rates of up to tens of body lengths per second, causing their accumulation at frontal zones. This mechanism explains how oceanic fronts become major feeding grounds for predators and targets for fishermen.

In situ observation of bainite growth during isothermal holding

The mechanism of bainite growth has been investigated using in situ transmission electron microscopy observations. It was found that, in a number of alloys studied, a bainitic embryo is made of basic transformation units. These units are either a group of stacking faults or, in two dimensions, a series of parallelograms of different sizes. Thickening/widening of the bainite embryo takes place through shear along the stacking fault planes or twining planes. The bainite embryo is elongated by the formation of new transformation units at both tips of the bainite plate. The three-dimensional morphology of bainite is a convex tens-like lath. It is believed that the bainite embryo grows by shearing, which is controlled by the diffusion of solute atoms during the transformation. As the growth rate is much lower than that of martensite, it is therefore detectable. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Non-coding RNA

The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.

Spin-detection in a quantum electromechanical shuttle system

We study the electrical transport of a harmonically bound, single-molecule C-60 shuttle operating in the Coulomb blockade regime, i.e. single electron shuttling. In particular, we examine the dependance of the tunnel current on an ultra-small stationary force exerted on the shuttle. As an example, we consider the force exerted on an endohedral N@C-60 by the magnetic field gradient generated by a nearby nanomagnet. We derive a Hamiltonian for the full shuttle system which includes the metallic contacts, the spatially dependent tunnel couplings to the shuttle, the electronic and motional degrees of freedom of the shuttle itself and a coupling of the shuttle's motion to a phonon bath. We analyse the resulting quantum master equation and find that, due to the exponential dependence of the tunnel probability on the shuttle-contact separation, the current is highly sensitive to very small forces. In particular, we predict that the spin state of the endohedral electrons of N@C-60 in a large magnetic gradient field can be distinguished from the resulting current signals within a few tens of nanoseconds. This effect could prove useful for the detection of the endohedral spin-state of individual paramagnetic molecules such as N@C-60 and P@C-60, or the detection of very small static forces acting on a C-60 shuttle.

Generic Technique to Generate Large Branched DNA Complexes

The inherent self-recognition properties of DNA have led to its use as a scaffold for various nanotechnology self-assembly applications, with macromolecular complexes, metallic and semiconducting nanoparticles, proteins, inter alia, being assembled onto a designed DNA scaffold. Such structures may typically comprise a number of DNA molecules organized into macromolecules. Many studies have used synthetic methods to produce the constituent DNA molecules, but this typically constrains the molecules to be no longer than around 100 base pairs (30 nm). However, applications that require larger self-assembling DNA complexes, several tens of nanometers or more, need to be generated by other techniques. Here, we present a generic technique to generate large linear, branched, and/or circular DNA macromolecular complexes. The effectiveness of this technique is demonstrated here by the use of Lambda Bacteriophage DNA as a template to generate single- and double-branched DNA structures approximately 120 nm in size.

40Ar/39Ar geochronological constraints on the evolution of lateritic iron deposits in the Quadrilatero Ferrifero, Minas Gerais, Brazil

Weathering profiles overlying the Sapecado, Pico and Andaime iron ore deposits, Quadrilátero Ferrífero (QF), Minas Gerais, Brazil, reach depths of 150–400 m and host world-class supergene iron orebodies. In addition to hosting supergene ore bodies of global economic significance, weathered banded iron-formations at the Quadrilátero Ferrífero and elsewhere (e.g., Carajás, Hamersley) are postulated to underlie some of the most ancient continuously exposed weathering profiles on earth. Laser incremental-heating 40Ar/39Ar results for 69 grains of hollandite-group manganese oxides extracted from 23 samples collected at depths ranging from 5 to 150 m at the Sapecado, Pico and Andaime deposits reveal ages ranging from ca. 62 to 14 Ma. Older Mn-oxides occur near the surface, while younger Mn-oxides occur at depth. However, many samples collected at the weathering–bedrock interface yield ages in the 51–41 Ma range, suggesting that the weathering profiles in the Quadrilátero Ferrífero had already reached their present depth in the Paleogene. The antiquity of the weathering profiles in the Quadrilátero Ferrífero is comparable to the antiquity of dated weathering profiles on banded iron-formations in the Carajás Region (Brazil) and the Hamersley Province, Western Australia. The age versus depth distributions obtained in this study, but not available for other regions containing similar supergene iron deposits, suggest that little further advance of the weathering front has occurred in the Quadrilátero Ferrífero lateritic profiles during the Neogene. The results suggest that weathering in some of these ancient landscapes is not controlled by the steady-state advance of weathering fronts through time, but may reflect climatic and geomorphological conditions prevailing in a remote past. The geochronological results also confirm that the ancient landsurfaces in the Quadrilátero Ferrífero probably remained immune to erosion for tens of millions of years. Deep weathering, mostly in the Paleogene, combined with low erosion rates, account for the abundance and widespread distribution of supergene iron, manganese, and aluminum orebodies in this region.