bluuebunny/crossref_metadata_2025 huggingface dataset:
Vegetative Characteristics of Recently Reforested Bottomlands in the Lower Cache River Watershed, Illinois, U.S.A.
Authors: Kruse Brian S. , Groninger John W.
Published: August 2003

AbstractInterest in restoring native ecosystems is resulting in conversion of marginal agricultural lands to bottomland hardwood‐dominated forests in the midwestern and midsouthern United States. Growing stock for these efforts typically consists of planted oak (Quercusspp.) and volunteer vegetation. Reports of mixed reforestation success and the lack of post‐establishment tree growth data prompted this evaluation of vegetation characteristics of 5‐ to 7‐year‐old operational restorations in the Lower Cache River Watershed in southernmost Illinois, U.S.A.Fraxinus pennsylvanica(green ash),Acer negundo(box‐elder), andLiquidambar styraciflua(sweetgum) together comprised 77% of all tree stems observed. Full stocking of overstory tree species can be expected to produce a closed canopy stand within 160 m of a forested edge, due primarily to the abundance of rapidly growing volunteer‐origin trees. Planted oaks contributed minimally to total tree stocking but were present in sufficient numbers to eventually improve wildlife habitat, and therefore satisfied restoration objectives. Oak height was 23% greater when in the presence of a non‐oak tree species. Herbaceous cover was dominated bySolidago gigantea(late goldenrod) andJuncusspp. (rushes).Solidago giganteawas associated with poor growth and low density of non‐oak stems, whereasJuncus dudleyi(Dudley's rush) was associated with taller non‐oak stems. These results suggest that the presence of volunteer‐origin trees is crucial for the creation of full stand stocking that will result in rapid development of a closed canopy forest. Improved success of future reforestation efforts will require more intensive methods to establish adequate stocking beyond 160 m of a forest edge. Methods described here could be adapted for agricultural field to forest restorations in other regions to predict critical distances from volunteer seed sources within which supplemental planting would be unnecessary to meet tree stocking objectives.
A Comparison of Remote Sensing and Ground‐Based Methods for Monitoring Wetland Restoration Success
Authors: Shuman Craig S. , Ambrose Richard F.
Published: August 2003

Abstract Efficient and accurate vegetation sampling techniques are essential for the assessment of wetland restoration success. Remotely acquired data, used extensively in many locations, have not been widely used to monitor restored wetlands. We compared three different vegetation sampling techniques to determine the accuracy associated with each method when used to determine species composition and cover in restored Pacific coast wetlands dominated by Salicornia virginica (perennial pickleweed). Two ground‐based techniques, using quadrat and line intercept sampling, and a remote sensing technique, using low altitude, high resolution, color and color infrared photographs, were applied to estimate cover in three small restoration sites. The remote technique provided an accurate and efficient means of sampling vegetation cover, but individual species could not be identified, precluding estimates of species density and distribution. Aerial photography was determined to be an effective tool for vegetation monitoring of simple (i.e., single‐species) habitat types or when species identities are not important (e.g., when vegetation is developing on a new restoration site). The efficiency associated with these vegetation sampling techniques was dependent on the scale of the assessment, with aerial photography more efficient than ground‐based sampling methods for assessing large areas. However, the inability of aerial photography to identify individual species, especially mixed‐species stands common in southern California salt marshes, limits its usefulness for monitoring restoration success. A combination of aerial photography and ground‐based methods may be the most effective means of monitoring the success of large wetland restoration projects.
Long‐Term Trends in Faunal Recolonization After Bauxite Mining in the Jarrah Forest of Southwestern Australia
Authors: Nichols Owen G. , Nichols Flora M.
Published: August 2003

Abstract Fauna serve a key role in many forest ecological processes. Despite this, few studies have considered long‐term faunal recolonization after mining and rehabilitation of forest ecosystems. In the jarrah forest of southwestern Australia, permanent fauna monitoring sites have been established in bauxite mined areas rehabilitated in 1990 and in a range of representative unmined forest control sites. At each site mammals, birds, reptiles, and ants were surveyed in 1992, 1995, and 1998. The aims of the monitoring were to develop a better understanding of faunal recolonization trends, to produce recommendations for promoting fauna return, and to consider which techniques and fauna groups are best suited for monitoring recolonization. The results showed that successional trends varied between fauna groups. Generalist foraging mammals recolonized rapidly, whereas small predators took longer. Feral mice were initially abundant and then declined. Birds gradually recolonized, and after 8 years bird communities were very similar to those in unmined forest sites. Reptile species took longer, and after 8 years numbers of species remained lower than in unmined forests. Species richness and diversity of ants in 8‐year‐old rehabilitation were comparable with those of unmined forest in some rehabilitated sites but were lower in others. The composition of ant communities was still different from that of unmined sites. Ant species that only use disturbed forest declined rapidly in abundance as rehabilitation aged. The results suggest that although the rates of faunal recolonization will vary, with time most or all mammal, bird, reptile, and ant species should inhabit rehabilitated bauxite mines. The densities of many are likely to be similar to those in unmined forest, but for others it is too early to know whether this will be the case. Techniques for promoting fauna return are discussed. This study demonstrates that no single fauna group is suitable for use as an overall “indicator” of faunal recolonization; different fauna species and groups reflect different aspects of faunal succession.
Spoil Heaps From Brown Coal Mining: Technical Reclamation Versus Spontaneous Revegetation
Authors: Hodačová Darina , Prach Karel
Published: August 2003

Abstract Vegetation samples from either spontaneously revegetated or technically reclaimed spoil heaps of different ages in one of the largest active brown coal mining districts in Europe were analyzed and compared. The spoil heaps are located in the northwestern part of the Czech Republic and represent ages between 0 and 45 years. Ordination analysis (detrended correspondence analysis) showed that vegetation on technically reclaimed spoil heaps developed in a different way than that on spontaneously revegetated ones. The latter exhibited much higher species diversity in the oldest stages with the number of species doubled that of technically reclaimed sites. The oldest stages were also more advanced along an expected successional gradient as indicated by the ordination. Accelerating the vegetation development by technical reclamation was only of temporal character, whereas spontaneous succession proceeded further over the longer time scale. Spontaneous succession is advocated as an inexpensive and easy alternative to technical reclamation, because it leads to a more natural and rich vegetation cover. Unfortunately, technical reclamation is still the only approach considered in the present reclamation activities for this region.
Effects of Prescribed Burning on Herbaceous and Woody Vegetation in Northern Lowland Meadows
Authors: Quinlan Allyson , Dale Mark R. T. , Gates C. Cormack
Published: August 2003

Abstract Spring burning of sedge‐grass meadows in the Slave River Lowlands (SRL), Northwest Territories, Canada was applied between 1992 and 1998 to reduce shrub encroachment and enhance Bison bison (bison) habitat, although the impact of fire on preferred bison forage was unknown before management. In the summer of 1998 we conducted a study in the Hook Lake area of the SRL to test the effect of burn frequency (unburned, burned once, or burned three times since 1992) on herbaceous plant community composition and Salix spp. L. (willow) shrub vigor. Plant species abundance, litter biomass, soil pH, and depth of the organic soil horizon were measured in 300 1‐m2 quadrats nested within 30 1,000‐m2 plots in both burned and unburned dry meadows. To test the relationship between frequency and willow vigor, all willow shrubs within the plots were assigned a vigor score from I (dead) to IV (flourishing). The spring burns appear to have reduced willow vigor; however, shrub survival remained high (76%) on the most frequently burned meadows. Ordination plots resulting from canonical correspondence analysis suggest that multiple spring burns influenced plant community composition in dry meadow areas and that less palatable bison forage species (e.g., Carex aenea Fern. and Juncus balticus L.) were correlated with a regime of three spring burns. Our results suggest that frequent spring fires in the Hook Lake area have only a small negative effect on willow cover but may reduce the abundance of primary bison forage plants compared with less frequently burned meadows.
The Importance of Phytogenic Mounds (Nebkhas) for Restoration of Arid Degraded Rangelands in Northern Sinai
Authors: El‐Bana Magdy I. , Nijs Ivan , Khedr Abdel‐Hamid A.
Published: August 2003

Abstract Natural accumulation of wind‐borne sediments within or around the canopies of plants plays an important role in the ecological and evolutionary dynamics of many coastal and desert ecosystems. The formation of such phytogenic mounds (nebkhas) creates patches that can strongly influence the spatial distribution of plant and soil resources. In land restoration of arid and semiarid environments it is important to study the potential role of such biological patchiness that may provide sites for coexistence of species with different life and growth forms. Our main objective was to test whether the nebkhas of a leguminous shrub, Retama raetam (white broom), promote restoration of herbaceous vegetation and soil in the degraded rangelands of northern Sinai. Vegetation and microclimatic and edaphic characteristics within the nebkhas, as well as within internebkha spaces, were compared for ungrazed and grazed sites. Abundance and richness of herbaceous plants were positively related to nebkha area, which explained more of the variance of abundance and richness in the grazed site than in the ungrazed one. Protection from grazing, especially on nebkhas, was associated with an increase in abundance and richness of herbaceous plants, improved soil microclimate, and increased soil fine particles and nutrient concentrations. The results suggest that management (in casu protection from grazing) of nebkhas of woody perennial shrubs changes rangeland conditions and improves the resource regulatory processes. Furthermore, nebkhas of unpalatable plants have the potential to preserve plant diversity in overgrazed plant communities, because they are effective in capturing and retaining water, soil materials, and propagules within and from nearby areas, resources that would otherwise be lost.
Restoration of Species Richness in Abandoned Mediterranean Grasslands: Seeds in Cattle Dung
Authors: Traba Juan , Levassor Catherine , Peco Begoña
Published: August 2003

Abstract Endozoochory has proven to be a highly effective mechanism in the dispersal of viable seeds in Mediterranean grasslands. We studied the effect of cattle dung application on species richness, particularly on the reintroduction of species lost after abandonment. Sown and control plots were monitored for 3 years after dung sowing. We found a significant increase in small‐scale richness, which may be attributed to the treatment, with the inclusion of species detected in the dung and in the grazed pasture. The differences in richness and floristic composition diminished over time. This experiment proves the potential utility of this treatment for the restoration of species richness in abandoned pastures, although supplementary steps are necessary, including further sowing and/or shrub cutting in subsequent years.
Managing Non‐Native Plant Populations Through Intensive Community Restoration in Cades Cove, Great Smoky Mountains National Park, U.S.A.
Authors: Price Charles A. , Weltzin Jake F.
Published: August 2003

AbstractCades Cove, Great Smoky Mountains National Park, U.S.A. was historically cleared largely for pastoral purposes; it is now comprised of recently abandoned pastures dominated by non‐native pasture species. To investigate the potential for reducing non‐native species relative to native species, park managers initiated an experiment in 1995 that included mowing, herbicide application, planting of seed, and burning of replicate 20 × 50–m plots at each of two sites within Cades Cove. Between 1995 and 2001 we evaluated the response of the plant community (i.e., species‐specific cover and frequency, biomass, diversity) to this suite of treatments and compared it with unmanipulated control plots at each site. Four years after treatment initiation abundance measures ofPlantago lanceolata,Setaria geniculata, andTrifoliumspp. averaged one‐third lower in treated than control plots. Frequency ofFestuca pratensiswas lower in treated than in control plots for 2 years, but after 4 years its frequency, cover, and biomass did not differ between treated and control plots. By 2000 the cover ofSorghastrum nutansin treated plots increased to 23–47%, depending on the site. Total biomass and diversity increased in treated plots. The dominance ofLespedeza cuneataat one site apparently reduced planting success, biomass production, and diversity and evenness. Post‐treatment lags in response for several species, coupled with interannual variation in response to environmental conditions, suggest that evaluations of treatment success would differ greatly depending on when the evaluation was conducted.
Surface diffraction studies of 2D crystals of short fatty alcohols at the air-water interface
Authors: Renault A. , Legrand J. F. , Goldmann M. , Berge B.
Published: August 2003

Using X ray surface diffraction we have investigated crystalline monolayers of short alcohols (1-decanol to 1-tetradecanol) at the air-water interface in the vicinity of the first order transition corresponding to 2D melting (Tm(2D)). The diffraction patterns in the solid phase are in agreement with a 2D hexagonal close-packing. The lattice parameter value is 5.00 Å just below Tm(2D) and amounts 4.90 Å at Tm(2D)-20 K. The resolution limited Bragg peaks indicate a large crystalline coherence length. At the approach of the 2D melting point, the observed increase of the Debye Waller factor is attributed to critical fluctuations.
Ultrasound scattering by buoyancy driven flows
Authors: Pinton J. F. , Laroche C. , Fauve S. , Baudet C.
Published: August 2003

We show experimentally that the scattering of sound by temperature inhomo-geneities may be used as a non-intrusive method to investigate the space-time characteristics of buoyancy-driven flows. We study the thermal plume generated in air by a horizontal hot wire as a test flow: we show that the onset of time-dependent instabilities as well as the advection of thermal inhomogeneities by the mean flow can be studied with our measurement technique.
Etude des mécanismes d'ionisation de H2O par interaction He*(2 1S, 2 3S)/Ne*(3P0, 3P2)+H2O
Authors: le Nadan André , Sinou Guillaume , Tuffin Firmin
Published: August 2003

Nous avons étudié l'ionisation Penning de H2O par des métastables 21S et 23S de l'hélium, ainsi que 3P0 et 3P2 du néon. Nous avons analysé l'énergie cinétique des ions créés au cours de la collision (parents et fragments). Afin d'interpréter certaines particularités expérimentales, l'hypothèse de transferts d'énergie de vibration en énergie cinétique est proposées. Par ailleurs, les caractéristiques des distributions en énergie des ions fragments sont expliquées par la prédissociation de l'état 2B2 de H2O+.
Molecular theory of order electricity
Authors: Osipov M. A. , Sluckin T. J.
Published: August 2003

The concept of order electricity has been employed by Durand, Barbero and colleagues to explain, in particular, the existence of equilibrium conical anchoring at liquid crystal interfaces. In this paper we examine this concept from a molecular point of view, using the density functional theory of liquid crystals. We show that the long range nature of the electrostatic force between molecules with permanent quadrupoles creates formal problems with rather profound consequences on the link between microscopic and macroscopic formulations of liquid crystal theory. One result is that the Landau-de Gennes gradient expansion must be employed with extreme caution in an inhomogeneous nematic. These formal problems have analogues in the theory of dielectrics and were explored by Ewald long ago. In addition we derive from a statistical mechanical viewpoint the phenomenological relations used to describe order electricity, and explore in detail the consequences of order electricity at an isotropic-nematic interface and at a nematic-substrate interface.
Dynamics of spontaneous emulsification
Authors: Granek R. , Ball R. C. , Cates M. E.
Published: August 2003

We present a model for spontaneous emulsification resulting from a transiently negative interfacial tension between water and oil regions, which may be achieved under conditions of strong adsorption of surfactant molecules to the interface. While our approach builds on a linear stability analysis, it addresses the essential non-linear coupling of surface growth to the diffusion flux of surfactants to the interface. We consider a large drop of oil of radius R embedded in a dilute surfactant solution and predict that undulations develop with a characteristic wavelength λ*, which at long times t obeys λ*∼t1/3. This suggests that the size of the droplets created spontaneously at the interface scales as ξo1/3, where ξo is a diffusion length which is comparable to R under steady state diffusion conditions. We discuss the regimes of applicability of our results to various experimental systems.
Columnar phase of pyramidic amphiphiles spread at the air-water interface
Authors: El Abed A. , Muller P. , Peretti P. , Gallet F. , Billard J.
Published: August 2003

Two compounds, forming thermotropic liquid-crystalline phases in the bulk, were spread at the air-water interface. For both compounds, the surface pressure versus molecular area diagrams exhibit a large domain of molecular areas where the surface pressure of the film is quasi-constant. This plateau region of the isotherms corresponds to a transition from a monolayer in a liquid-expanded phase to a metastable condensed monolayer in which the molecules may adopt an “edge-on” arrangement. In this arrangement, the base of the pyramidic core is normal to the air-water interface. The film was also observed by means of fluorescence and polarizing microscopy. These techniques allowed us to show the formation of anisotropic slowly growing multilayered domains from the “edge-on” monolayer. An original method, based on the light reflectivity of the domains, was developed to measure their thickness and their optical anisotropy. The results show that these domains are formed by an arrangement of the molecules in rectilinear columns for one compound and in spiral columns for the other compound.
Confinement of dilute solutions of living polymers
Authors: Schmitt V. , Lequeux F. , Marques C. M.
Published: August 2003

We investigate the thermodynamic properties of a dilute solution of living polymers confined between two solid repulsive walls. We consider both the case of rigid and of flexible macromolecules. When the confined system is taken to be at equilibrium with an external reservoir the living polymers behave similarly to a polydisperse solution of unbreakable chains. However for closed gaps the behaviour is quite different from a classical polymer solution because the worm-like micelles can adapt their intrinsic polydispersity in order to release the confinement constraint. In particular, for rigid living polymers this leads to a divergence of the average chain-length in the limit of strong confinement, as well as to a non-monotonic behaviour of the pressure acting on the walls.
Spiral textures in lyotropic liquid crystals : first order transition between normal hexagonal and lamellar gel phases
Authors: McGrath K. M. , Kékicheff P. , Kléman M.
Published: August 2003

The first order transition between the normal hexagonal phase (Hα) and lamellar gel phase (Lβ, Lβ', Lδ, ... type) in lyotropic liquid crystals of binary surfactant/water systems is investigated. Structural transformations and epitaxial relations are investigated by small-angle X-ray scattering on powdered and oriented samples. By slow evaporation of water, growth of the gel layered structure from the two-dimensional packing of surfactant cylinders of the hexagonal mesophase in the presence of a solid wall reveals a spectacular new texture composed of interwoven spirals. It is demonstrated that the layers grow from the rods of the hexagonal phase, in planes coplanar with the hexagonal packing and perpendicular to the wall. The configuration is such that line wedge disclinations of strength $s= +~1/2$ of the hexagonal phase are preserved through the phase transition. Estimates of the radii for the developable domain and cores, and also for the bending elastic constant are obtained. A mechanism for the phase transformation is discussed in view of topological structural transformations and a modification of the short-range order associated to the disorder order transition of the configuration of the paraffinic chains.
Visualizing infection of individual influenza viruses
Authors: Lakadamyali Melike , Rust Michael J. , Babcock Hazen P. , Zhuang Xiaowei
Published: August 2003

Influenza is a paradigm for understanding viral infections. As an opportunistic pathogen exploiting the cellular endocytic machinery for infection, influenza is also a valuable model system for exploring the cell's constitutive endocytic pathway. We have studied the transport, acidification, and fusion of single influenza viruses in living cells by using real-time fluorescence microscopy and have dissected individual stages of the viral entry pathway. The movement of individual viruses revealed a striking three-stage active transport process that preceded viral fusion with endosomes starting with an actin-dependent movement in the cell periphery, followed by a rapid, dynein-directed translocation to the perinuclear region, and finally an intermittent movement involving both plus- and minus-end-directed microtubule-based motilities in the perinuclear region. Surprisingly, the majority of viruses experience their initial acidification in the perinuclear region immediately following the dynein-directed rapid translocation step. This finding suggests a previously undescribed scenario of the endocytic pathway toward late endosomes: endosome maturation, including initial acidification, largely occurs in the perinuclear region.
Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis ofNeisseria meningitidisgroup B
Authors: Grifantini Renata , Sebastian Shite , Frigimelica Elisabetta , Draghi Monia , Bartolini Erika , Muzzi Alessandro , Rappuoli Rino , Grandi Guido , Genco Caroline Attardo
Published: August 2003

Iron is limiting in the human host, and bacterial pathogens respond to this environment by activating genes required for bacterial virulence. Transcriptional regulation in response to iron in Gram-negative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe DNA microarray, computational andin vitrostudies to define the Fur regulon in the human pathogenNeisseria meningitidisgroup B (strain MC58). After iron addition to an iron-depleted bacterial culture, 153 genes were up-regulated and 80 were down-regulated. Only 50% of the iron-regulated genes were found to contain Fur-binding consensus sequences in their promoter regions. Forty-two promoter regions were amplified and 32 of these were shown to bind Fur by gel-shift analysis. Among these genes, many of which had never been described before to be Fur-regulated, 10 were up-regulated on iron addition, demonstrating that Fur can also act as a transcriptional activator. Sequence alignment of the Fur-binding regions revealed that theN. meningitidisFur-box encompasses the highly conserved (NATWAT)3motif. Cluster analysis was effective in predicting Fur-regulated genes even if computer prediction failed to identify Fur-box-like sequences in their promoter regions. Microarray-generated gene expression profiling appears to be a very effective approach to define new regulons and regulatory pathways in pathogenic bacteria.
The human multidrug resistance protein MRP4 functions as a prostaglandin efflux transporter and is inhibited by nonsteroidal antiinflammatory drugs
Authors: Reid Glen , Wielinga Peter , Zelcer Noam , van der Heijden Ingrid , Kuil Annemieke , de Haas Marcel , Wijnholds Jan , Borst Piet
Published: August 2003

Prostaglandins are involved in a wide variety of physiological and
pathophysiological processes, but the mechanism of prostaglandin release from
cells is not completely understood. Although poorly membrane permeable,
prostaglandins are believed to exit cells by passive diffusion. We have
investigated the interaction between prostaglandins and members of the
ATP-binding cassette (ABC) transporter ABCC [multidrug resistance protein
(MRP)] family of membrane export pumps. In inside-out membrane vesicles
derived from insect cells or HEK293 cells, MRP4 catalyzed the time- and
ATP-dependent uptake of prostaglandin E
1
(PGE
1
) and
PGE
2
. In contrast, MRP1, MRP2, MRP3, and MRP5 did not transport
PGE
1
or PGE
2
. The MRP4-mediated transport of
PGE
1
and PGE
2
displayed saturation kinetics, with
K
m
values of 2.1 and 3.4 μM, respectively. Further
studies showed that PGF
1
α
,
PGF
2
α
, PGA
1
, and thromboxane
B
2
were high-affinity inhibitors (and therefore presumably
substrates) of MRP4. Furthermore, several nonsteroidal antiinflammatory drugs
were potent inhibitors of MRP4 at concentrations that did not inhibit MRP1. In
cells expressing the prostaglandin transporter PGT, the steady-state
accumulation of PGE
1
and PGE
2
was reduced proportional
to MRP4 expression. Inhibition of MRP4 by an MRP4-specific RNA interference
construct or by indomethacin reversed this accumulation deficit. Together,
these data suggest that MRP4 can release prostaglandins from cells, and that,
in addition to inhibiting prostaglandin synthesis, some nonsteroidal
antiinflammatory drugs might also act by inhibiting this release.
Skeletal muscle engraftment potential of adult mouse skin side population cells
Authors: Montanaro Federica , Liadaki Kalliopi , Volinski Jay , Flint Alan , Kunkel Louis M.
Published: August 2003

Adult bone marrow and skeletal muscle have been shown to contain a
subpopulation of cells, called side population (SP) cells, that can be
isolated with the fluorescence-activated cell sorter. We used a similar method
to identify SP cells in the skin of adult mice. These cells express surface
markers similar to SP cells isolated from skeletal muscle, but differ from
bone marrow SP cells and do not express hematopoietic markers. When
transplanted into nonirradiated
mdx
mice, nuclei from donor skin SP
cells are found within myofibers that express dystrophin. Thus, adult skin SP
cells can engraft in dystrophic skeletal muscle even in the absence of total
body irradiation.
Sexual dimorphism in
Australopithecus afarensis
was similar to that of modern humans
Authors: Reno Philip L. , Meindl Richard S. , McCollum Melanie A. , Lovejoy C. Owen
Published: August 2003

The substantial fossil record for
Australopithecus afarensis
includes both an adult partial skeleton [Afar Locality (A.L.) 288-1,
“Lucy”] and a large simultaneous death assemblage (A.L. 333). Here
we optimize data derived from both to more accurately estimate skeletal size
dimorphism. Postcranial ratios derived from A.L. 288-1 enable a significant
increase in sample size compared with previous studies. Extensive simulations
using modern humans, chimpanzees, and gorillas confirm that this technique is
accurate and that skeletal size dimorphism in
A. afarensis
was most
similar to that of contemporary
Homo sapiens
. These data eliminate
some apparent discrepancies between the canine and skeletal size dimorphism in
hominoids, imply that the species was not characterized by substantial sexual
bimaturation, and greatly increase the probability that the reproductive
strategy of
A. afarensis
was principally monogamy.
Single-molecule transition-state analysis of RNA folding
Authors: Bokinsky Gregory , Rueda David , Misra Vinod K. , Rhodes Maria M. , Gordus Andrew , Babcock Hazen P. , Walter Nils G. , Zhuang Xiaowei
Published: August 2003

How RNA molecules fold into functional structures is a problem of great
significance given the expanding list of essential cellular RNA enzymes and
the increasing number of applications of RNA in biotechnology and medicine. A
critical step toward solving the RNA folding problem is the characterization
of the associated transition states. This is a challenging task in part
because the rugged energy landscape of RNA often leads to the coexistence of
multiple distinct structural transitions. Here, we exploit single-molecule
fluorescence spectroscopy to follow in real time the equilibrium transitions
between conformational states of a model RNA enzyme, the hairpin ribozyme. We
clearly distinguish structural transitions between effectively
noninterchanging sets of unfolded and folded states and characterize key
factors defining the transition state of an elementary folding reaction where
the hairpin ribozyme's two helical domains dock to make several tertiary
contacts. Our single-molecule experiments in conjunction with site-specific
mutations and metal ion titrations show that the two RNA domains are in a
contact or close-to-contact configuration in the transition state even though
the native tertiary contacts are at most partially formed. Such a compact
transition state without well formed tertiary contacts may be a general
property of elementary RNA folding reactions.
The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease
Authors: Wilson Mark A. , Collins Jennifer L. , Hod Yaacov , Ringe Dagmar , Petsko Gregory A.
Published: August 2003

Mutations inDJ-1, a human gene with homologues in organisms from all kingdoms of life, have been shown to be associated with autosomal recessive, early onset Parkinson's disease (PARK7). We report here the three-dimensional structure of the DJ-1 protein, determined at a resolution of 1.1 Å by x-ray crystallography. The chain fold of DJ-1 resembles those of a bacterial protein, PfpI, that has been annotated as a cysteine protease, and of a domain of a bacterial catalase whose role in the activity of that enzyme is uncertain. In contrast to PfpI, a hexameric protein whose oligomeric structure is essential for its putative proteolytic activity, DJ-1 is a dimer with completely different intersubunit contacts. The proposed catalytic triad of PfpI is absent from the corresponding region of the structure of DJ-1, and biochemical assays fail to detect any protease activity for purified DJ-1. A highly conserved cysteine residue, which is catalytically essential in homologues of DJ-1, shows an extreme sensitivity to radiation damage and may be subject to other forms of oxidative modification as well. The structure suggests that the loss of function caused by the Parkinson's-associated mutation L166P in DJ-1 is due to destabilization of the dimer interface. Taken together, the crystal structure of human DJ-1 plus other observations suggest the possible involvement of this protein in the cellular oxidative stress response and a general etiology of neurodegenerative diseases.
Escherichia coli single-stranded DNA-binding protein mediates template recycling during transcription by bacteriophage N4 virion RNA polymerase
Authors: Davydova Elena K. , Rothman-Denes Lucia B.
Published: August 2003

Coliphage N4 virion RNA polymerase (vRNAP), the most distantly related
member of the T7-like family of RNA polymerases, is responsible for
transcription of the early genes of the linear double-stranded DNA phage
genome.
Escherichia coli
single-stranded DNA-binding protein
(
Eco
SSB) is required for N4 early transcription
in vivo
, as
well as for
in vitro
transcription on super-coiled DNA templates
containing vRNAP promoters. In contrast to other DNA-dependent RNA
polymerases, vRNAP initiates transcription on single-stranded,
promoter-containing templates with
in vivo
specificity; however, the
RNA product is not displaced, thus limiting template usage to one round. We
show that
Eco
SSB activates vRNAP transcription at limiting
single-stranded template concentrations through template recycling.
Eco
SSB binds to the template and to the nascent transcript and
prevents the formation of a transcriptionally inert RNA:DNA hybrid. Using
C-terminally truncated
Eco
SSB mutant proteins, human mitochondrial
SSB (
Hs
mt SSB), phage P1 SSB, and F episome-encoded SSB, as well as a
Hs
mt-
Eco
SSB chimera, we have mapped a determinant of
template recycling to the C-terminal amino acids of
Eco
SSB. T7 RNAP
contains an amino-terminal domain responsible for binding the RNA product as
it exits from the enzyme. No sequence similarity to this domain exists in
vRNAP. Hereby, we propose a unique role for
Eco
SSB: It functionally
substitutes in N4 vRNAP for the N-terminal domain of T7 RNAP responsible for
RNA binding.
Neuronal depletion of calcium-dependent proteins in the dentate gyrus is tightly linked to Alzheimer's disease-related cognitive deficits
Authors: Palop Jorge J. , Jones Brian , Kekonius Lisa , Chin Jeannie , Yu Gui-Qiu , Raber Jacob , Masliah Eliezer , Mucke Lennart
Published: August 2003

Transgenic mice expressing human amyloid precursor proteins (hAPP) and
amyloid-β peptides (Aβ) in neurons develop phenotypic alterations
resembling Alzheimer's disease (AD). The mechanisms underlying cognitive
deficits in AD and hAPP mice are largely unknown. We have identified two
molecular alterations that accurately reflect AD-related cognitive
impairments. Learning deficits in mice expressing familial AD-mutant hAPP
correlated strongly with decreased levels of the calcium-binding protein
calbindin-D
28k
(CB) and the calcium-dependent immediate early gene
product c-Fos in granule cells of the dentate gyrus, a brain region critically
involved in learning and memory. These molecular alterations were
age-dependent and correlated with the relative abundance of Aβ1–42
but not with the amount of Aβ deposited in amyloid plaques. CB reductions
in the dentate gyrus primarily reflected a decrease in neuronal CB levels
rather than a loss of CB-producing neurons. CB levels were also markedly
reduced in granule cells of humans with AD, even though these neurons are
relatively resistant to AD-related cell death. Thus, neuronal populations
resisting cell death in AD and hAPP mice can still be drastically altered at
the molecular level. The tight link between Aβ-induced cognitive deficits
and neuronal depletion of CB and c-Fos suggests an involvement of
calcium-dependent pathways in AD-related cognitive decline and could
facilitate the preclinical evaluation of novel AD treatments.
Stimulation of NeuroD activity by huntingtin and huntingtin-associated proteins HAP1 and MLK2
Authors: Marcora Edoardo , Gowan Katherine , Lee Jacqueline E.
Published: August 2003

NeuroD (ND) is a basic helix–loop–helix transcription factor
important for neuronal development and survival. By using a yeast two-hybrid
screen, we identified two proteins that interact with ND,
huntingtin-associated protein 1 (HAP1) and mixed-lineage kinase 2 (MLK2), both
of which are known to interact with huntingtin (Htt). Htt is a ubiquitous
protein important for neuronal transcription, development, and survival, and
loss of its function has been implicated in the pathogenesis of Huntington's
disease, a neurodegenerative disorder. However, the mechanism by which Htt
exerts its neuron-specific function at the molecular level is unknown. Here we
report that Htt interacts with ND via HAP1, and that MLK2 phosphorylates and
stimulates the activity of ND. Furthermore, we show that Htt and HAP1
facilitate the activation of ND by MLK2. To our knowledge, ND is the first
example of a neuron-specific transcription factor involved in neuronal
development and survival whose activity is modulated by Htt. We propose that
Htt, together with HAP1, may function as a scaffold for the activation of ND
by MLK2.
Tufted puffin reproduction reveals ocean climate variability
Authors: Gjerdrum Carina , Vallée Anne M. J. , St. Clair Colleen Cassady , Bertram Douglas F. , Ryder John L. , Blackburn Gwylim S.
Published: August 2003

Anomalously warm sea-surface temperatures (SSTs) are associated with interannual and decadal variability as well as with long-term climate changes indicative of global warming. Such oscillations could precipitate changes in a variety of oceanic processes to affect marine species worldwide. As global temperatures continue to rise, it will be critically important to be able to predict the effects of such changes on species' abundance, distribution, and ecological relationships so as to identify vulnerable populations. Off the coast of British Columbia, warm SSTs have persisted through the last two decades. Based on 16 years of reproductive data collected between 1975 and 2002, we show that the extreme variation in reproductive performance exhibited by tufted puffins (Fratercula cirrhata) was related to changes in SST both within and among seasons. Especially warm SSTs corresponded with drastically decreased growth rates and fledging success of puffin nestlings. Puffins may partially compensate for within-season changes associated with SST by adjusting their breeding phenology, yet our data also suggest that they are highly vulnerable to the effects of climate change at this site and may serve as a valuable indicator of biological change in the North Pacific. Further and prolonged increases in ocean temperature could make Triangle Island, which contains the largest tufted puffin colony in Canada, unsuitable as a breeding site for this species.
Two previously undescribed members of the mouse CPEB family of genes and their inducible expression in the principal cell layers of the hippocampus
Authors: Theis Martin , Si Kausik , Kandel Eric R.
Published: August 2003

Cytoplasmic polyadenylation element-binding (CPEB) proteins control
polyadenylation-induced translation in early development. Studies in oocytes
led to the delineation of
Xenopus
CPEB, the first member of the
family to be identified, and its mouse homologue mCPEB-1. Recently, a second
mouse family member, mCPEB-2, has been described in germ cells. Increasing
evidence also implicates CPEB proteins as being important in the hippocampus,
where these proteins are thought to regulate local protein synthesis and
synaptic plasticity. We therefore carried out a systematic screen for CPEB
genes in the mouse brain and report two previously undescribed gene family
members: mCPEB-3 and -4. We next examined the expression of all four genes in
the hippocampus and found that mCPEB-1, -2, and -4 transcripts are expressed
in the principal cell layer in the CA3 and CA1 region and in the dentate gyrus
of the hippocampus. mCPEB-3 was barely expressed in naïve animals but
together with mCPEB-4 was strongly up-regulated after injection of kainate to
initiate seizure activity. Whereas mCPEB-1 is regulated by the Aurora kinase,
mCPEB-2, -3, and -4 do not contain Aurora kinase phosphorylation sites.
However, alternative splice isoforms of mCPEB-2, -3, and -4 encode the
so-called B region with phosphorylation sites for cAMP-dependent protein
kinase, calcium/calmodulin-dependent protein kinase II, and S6 kinase. Only
isoforms that encode the B region were expressed in the principal cell layer.
Coexpression of mCPEB-1 and the B region-containing splice isoforms suggests
that a variety of different signaling pathways can recruit CPEB activity in
hippocampal neurons.
Insig-1 “brakes” lipogenesis in adipocytes and inhibits differentiation of preadipocytes
Authors: Li Jinping , Takaishi Kiyosumi , Cook William , McCorkle Sara Kay , Unger Roger H.
Published: August 2003

We have examined gene expression in the fat tissue of normal mice at the
onset of diet-induced obesity. Insulin-induced gene 1 (insig-1) mRNA rose
progressively with a high-fat diet and declined on a restricted diet. Because
insig-1 binds sterol regulatory element-binding protein cleavage-activating
protein in the endoplasmic reticulum, thereby blocking proteolytic processing
required for sterol regulatory element-binding protein activation, we tested
its influence on lipogenesis. In differentiating 3T3-L1 cells, insig-1 and -2
rose in parallel with aP
2
mRNA during differentiation. The mRNA of
the lipogenic transcription factor, carbohydrate response element-binding
protein, was undetectable in undifferentiated 3T3-L1 preadipocytes but rose
dramatically during differentiation in 25 mM, but not in 5 mM, glucose.
Transfection of mouse or human insig-1 into 3T3-L1 preadipocytes completely
prevented oil red O staining and blocked upregulation of aP
2
,
peroxisome proliferator-activated receptor γ
2
, and
carbohydrate response element-binding protein, while reducing down-regulation
of preadipocyte factor 1. The results suggest that insig-1 expression
restricts lipogenesis in mature adipocytes and blocks differentiation in
preadipocytes.
Structural insights into the antigenicity of myelin oligodendrocyte glycoprotein
Authors: Breithaupt Constanze , Schubart Anna , Zander Hilke , Skerra Arne , Huber Robert , Linington Christopher , Jacob Uwe
Published: August 2003

Multiple sclerosis is a chronic disease of the central nervous system (CNS) characterized by inflammation, demyelination, and axonal loss. The immunopathogenesis of demyelination in multiple sclerosis involves an autoantibody response to myelin oligodendrocyte glycoprotein (MOG), a type I transmembrane protein located at the surface of CNS myelin. Here we present the crystal structures of the extracellular domain of MOG (MOGIgd) at 1.45-Å resolution and the complex of MOGIgdwith the antigen-binding fragment (Fab) of the MOG-specific demyelinating monoclonal antibody 8-18C5 at 3.0-Å resolution. MOGIgdadopts an IgV like fold with the A′GFCC′C″ sheet harboring a cavity similar to the one used by the costimulatory molecule B7-2 to bind its ligand CTLA4. The antibody 8-18C5 binds to three loops located at the membrane-distal side of MOG with a surprisingly dominant contribution made by MOG residues 101–108 containing a strained loop that forms the upper edge of the putative ligand binding site. The sequence R101DHSYQEE108is unique for MOG, whereas large parts of the remaining sequence are conserved in potentially tolerogenic MOG homologues expressed outside the immuno-privileged environment of the CNS. Strikingly, the only sequence identical to DHSYQEE was found in aChlamydia trachomatisprotein of unknown function, raising the possibility thatChlamydiainfections may play a role in the MOG-specific autoimmune response in man. Our data provide the structural basis for the development of diagnostic and therapeutic strategies targeting the pathogenic autoantibody response to MOG.
Amplification of xenon NMR and MRI by remote detection
Authors: Moulé Adam J. , Spence Megan M. , Han Song-I , Seeley Juliette A. , Pierce Kimberly L. , Saxena Sunil , Pines Alexander
Published: August 2003

A technique is proposed in which an NMR spectrum or MRI is encoded and
stored as spin polarization and is then moved to a different physical location
to be detected. Remote detection allows the separate optimization of the
encoding and detection steps, permitting the independent choice of
experimental conditions and excitation and detection methodologies. In the
initial experimental demonstration of this technique, we show that taking
dilute
129
Xe from a porous sample placed inside a large encoding
coil and concentrating it into a smaller detection coil can amplify NMR
signal. In general, the study of NMR active molecules at low concentration
that have low physical filling factor is facilitated by remote detection. In
the second experimental demonstration, MRI information encoded in a very
low-field magnet (4–7 mT) is transferred to a high-field magnet (4.2 T)
to be detected under optimized conditions. Furthermore, remote detection
allows the utilization of ultrasensitive optical or superconducting quantum
interference device detection techniques, which broadens the horizon of NMR
experimentation.
Importance of low-oligomeric-weight species for prion propagation in the yeast prion system Sup35/Hsp104
Authors: Narayanan Saravanakumar , Bösl Benjamin , Walter Stefan , Reif Bernd
Published: August 2003

The [
PSI
+
] determinant of
Saccharomyces
cerevisiae
, consisting of the cytosolic translation termination factor
Sup35, is a prion-type genetic element that induces an inheritable
conformational change and converts the Sup35 protein into amyloid fibers. The
molecular chaperone Hsp104 is required to maintain self-replication of
[
PSI
+
]. We observe
in vitro
that addition of
catalytic amounts of Hsp104 to the prion-determining region of the NM domain
of Sup35, Sup35
5–26
, results in the dissociation of
oligomeric Sup35 into monomeric species. Several intermediates of
Sup35
5–26
could be detected during this process. Strong
interactions are found between Hsp104 and hexameric/tetrameric
Sup35
5–26
, whereas the intermediate and monomeric
“release” forms show a decreased affinity with respect to Hsp104,
as monitored by saturation transfer difference and diffusion-ordered NMR
spectroscopic experiments. Interactions are mediated mostly by the side chains
of Gln, Asn, and Tyr residues in Sup35
5–26
. No interaction
can be detected between Hsp104 and higher oligomeric states (≥8) of
Sup35
5–26
. Taking into account the fact that Hsp104 is
required for maintenance of [
PSI
+
], we suggest that
low-oligomeric-weight species of Sup35 are important for prion propagation in
yeast.
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
Authors: Tan Elliot , Wilson Timothy J. , Nahas Michelle K. , Clegg Robert M. , Lilley David M. J. , Ha Taekjip
Published: August 2003

The natural form of the hairpin ribozyme comprises two major structural
elements: a four-way RNA junction and two internal loops carried by adjacent
arms of the junction. The ribozyme folds into its active conformation by an
intimate association between the loops, and the efficiency of this process is
greatly enhanced by the presence of the junction. We have used single-molecule
spectroscopy to show that the natural form fluctuates among three distinct
states: the folded state and two additional, rapidly interconverting states
(proximal and distal) that are inherited from the junction. The proximal state
juxtaposes the two loop elements, thereby increasing the probability of their
interaction and thus accelerating folding by nearly three orders of magnitude
and allowing the ribozyme to fold rapidly in physiological conditions.
Therefore, the hairpin ribozyme exploits the dynamics of the junction to
facilitate the formation of the active site from its other elements. Dynamic
interplay between structural elements, as we demonstrate for the hairpin
ribozyme, may be a general theme for other functional RNA molecules.