bluuebunny/crossref_metadata_2025 huggingface dataset:
Generating Policies for Sustainable Water Use in Complex Scenarios: An Integrated Land-Use and Water-Use Model of Monroe County, Michigan
Authors: Zellner Moira L
Published: March 2007

Rapidly declining groundwater levels since the early 1990s have raised serious concern in Monroe County, Michigan. Hydrological studies suggest that land-use changes have caused this decline. The mechanisms linking land-use and groundwater dynamics are not clear, however. In this paper I present WULUM, the Water-Use and Land-Use Model, an agent-based model that serves as an analytical framework to understand how these processes interact to create the observed patterns of resource depletion, and to suggest policies to reverse the process. The land-use component includes the main groundwater extractors in the county—stone quarries, golf courses, farms, and households. The groundwater component includes the glacial deposits and the underlying bedrock acquifer. The behavior of water users is defined by simple rules that determine their location and consumption. The dynamics of groundwater are represented through infiltration and diffusion rules between each cell and its immediate neighbors. Initial explorations with the model showed that land-use patterns contributed significantly to groundwater declines, while eliminating quarry dewatering did not entirely solve the problem. Both low-density and high-density zoning restrictions improved aquifer conditions over medium-density development, suggesting a nonlinear relationship between intensity of residential use and groundwater levels. Moreover, of all the natural and policy variables, zoning had the greatest influence on urban settlement and therefore on resource consumption.
Hinge versus Twist: The Effects of ‘Reference Surfaces’ and Discontinuities on Stereoscopic Slant Perception
Authors: Gillam Barbara , Blackburn Shane , Brooks Kevin
Published: March 2007

Stereoscopic slant perception around a vertical axis (horizontal slant) is often found to be strongly attenuated relative to geometric prediction. Stereo slant is much greater, however, when an adjacent surface, stereoscopically in the frontal plane, is added. This slant enhancement is often attributed to the presence of a ‘reference surface’ or to a spatial change in the disparity gradient (introducing second and higher derivatives of disparity). Gillam, Chambers, and Russo (1988 Journal of Experimental Psychology: Human Perception and Performance14 163–175) questioned the role of these factors in that placement of the frontal-plane surface in a direction collinear with the slant axis (twist configuration) sharply reduced latency for perceiving slant whereas placing the same surface in a direction orthogonal to the slant axis (hinge configuration) had little effect. We here confirm these findings for slant magnitude, showing a striking advantage for twist over hinge configurations. We also examined contrast slant measured on the frontal-plane surface in the hinge and twist configurations. Under conditions where test and inducer surfaces have centres at the same depth for twist and hinge, we found that twist configurations produced strong negative slant contrast, while hinge configurations produced significant positive contrast or slant assimilation. We conclude that stereo slant and contrast effects for neighbouring surfaces can only be understood from the patterns and gradients of step disparities present. It is not adequate to consider the second surface merely as a reference slant for the first or as having its effect via a spatial change in the disparity gradient.
A specialised soil corer for sampling tree roots
Authors: Sochacki Stanley , Ritson Peter , Brand Bruce
Published: March 2007

Sampling and measurement of tree root systems is arduous, expensive, and time-consuming. The lack of adequate and efficient equipment has resulted in the development of a new soil-root sampling apparatus which is able to sample tree roots of any diameter and soils of any hardness. This apparatus is inexpensive, compact, manoeuvrable, and very versatile in application.
Indexing soil quality: a new paradigm in soil science research
Authors: Erkossa Teklu , Itanna Fisseha , Stahr Karl
Published: March 2007

Soil quality indexing is a new approach in spatial and temporal evaluation of land management systems effects on soils’ capacity to function. A field experiment was conducted at Caffee Doonsa (2400 m a.s.l., 08°57′N, 39°06′E) for 6 years (1998–2003) to compare the effects of land preparation methods on soil quality (SQ) and to test the use of the Soil Management Assessment Framework (SMAF) in assessing SQ under the Ethiopian Central Highlands conditions. Four methods of land preparation [broad bed and furrows (BBF), green manure (GM), ridge and furrows (RF), and reduced tillage (RT)] were arranged in a randomised complete block design with 3 replications on permanent plots (22 m by 6 m). Physical, chemical, and biological SQ indicators were determined and scored, and a soil quality index (SQI) was developed using the SMAF procedures. Seven SQ indicators including microbial biomass carbon (MBC), bulk density, aggregate stability (AGG), soil organic carbon (Corg), pH, available water capacity (AWC), and available phosphorus were selected as a minimum dataset. The scored values of the indicators ranged from 0.21 for AGG and 0.97 for pH, both under BBF. Compared with RF (control), all the alternatives (GM, BBF, and RT) increased the scores of Corg and MBC. Moreover, BBF and GM increased the score values of AWC and AGG, respectively. Consequently, there was a non-significant increase in SQI due to the use of GM, BBF, and RT compared with the control. As a result, the land preparation methods may be preferred in a decreasing order GM ≥ BBF ≥ RT ≥ RF for the management goal of crop production. The study indicated that SMAF could be a robust tool to assess the performance of land management methods on soil quality in the study area, but some modifications may be required to fit to the prevailing cropping system and soil characteristics.
Sandblasting damage of narrow-leaf lupin (Lupinus angustifolius L.): a field wind tunnel simulation
Authors: Bennell M. R. , Leys J. F. , Cleugh H. A.
Published: March 2007

Lupins are frequently the preferred legume species used in dryland crop rotations on light sandy soil types. These soils are prone to erode and the probability of sandblasting is increased if sown to lupins because of their slow growth and low vegetative cover during establishment. In addition, lupins are vulnerable to sandblasting, having above-ground growing points in contrast to cereals where the meristem is below ground and sheltered from damage unless erosion is severe. Consequently, there is concern about sandblasting having an economic impact on farming returns by causing yield reduction in lupin crops. This study reports the impact on the development and yield of narrow-leaf lupins exposed to different durations of sandblasting at a constant wind speed. A portable wind tunnel was placed in the field generating a turbulent boundary layer with a constant free stream mean velocity of 13.7 m/s. Field-grown plants of narrow-leaf lupin (cv. Merrit) were exposed to this velocity field with a total transport mass of 0, 42, 78, 153, and 248 kg/m achieved by maintaining a constant rate of soil introduction and increasing the run time. Plants with an average leaf number of 3.4–9.7 showed macro-damage symptoms increasing in severity with increased transport mass. Yield reduction was not significant up to a total transport mass of 78 kg/m at which plants were showing damage symptoms of wilting and burning of immature leaves and with minor damage of mature leaves. As levels of total transport mass increased, yield reduction occurred, until at the maximum treatment level of 248 kg/m, there was an 18% grain yield loss. At this treatment level damage symptoms included loss of most of the leaf tissue and scoring of the stem. These results indicate that sandblasting can cause significant yield reductions in lupin and that measures to control soil erosion through minimum tillage practices or windbreaks should be considered.
Phosphorus accumulation and other changes in soil properties as a consequence of vegetable production, Sydney region, Australia
Authors: Chan K. Y. , Dorahy C. G. , Tyler S. , Wells A. T. , Milham P. P. , Barchia I.
Published: March 2007

A survey of 34 farms covering the major soil types used for growing vegetables within the greater Sydney metropolitan region (New South Wales, Australia) was undertaken to determine the effect of vegetable production on soil chemical and physical properties. Comparison of farmed ‘vegetable’ v. unfarmed ‘reference’ sites revealed that the soils used for vegetable production had extremely high concentrations of total P, Colwell-P, and CaCl2-extractable P (mean 1205, 224, and 4.3 mg/kg in the 0–0.30 m layer, respectively). In the 0–0.30 m soil layer, mean bicarbonate-extractable P (Colwell-P) concentrations have increased to up to 44 times that of the unfarmed reference soils and exceed that required for adequate vegetable nutrition. Concentrations of P in the soil solution (CaCl2-P) were up to 230 times that of the unfarmed reference soils. Moreover, the vegetable soils had low total soil carbon concentrations (mean 14.1 g/kg in the 0–0.10 m layer, only 57% of the mean concentration of the reference soils). These soils exhibited extremely low structural stability, which is likely to reduce soil infiltration rates and increase the potential for runoff. Marked changes in soil pH, EC, and exchangeable cations (Ca, Mg, and K) were also observed as a consequence of vegetable production.
All of these changes are a consequence of current management practices used in vegetable production, which include application of high rates of inorganic fertilisers and poultry manure, as well as excessive cultivation. Excessive accumulation of P, to at least 0.30 m depth, coupled with a loss of soil structural stability, is of particular environmental concern. Options such as adopting minimum tillage, in conjunction with using alternative inputs such as low P composts and cover crops, as a means of improving soil structure and reducing the extent of P accumulation in these soils require further investigation.
Assessment of the influence of soil structure on soil strength/soil wetness relationships on Red Ferrosols in north-west Tasmania
Authors: Cotching W. E. , Belbin K. C.
Published: March 2007

The relationship of soil wetness to soil strength in Red Ferrosols was compared between fields of well structured to degraded soil structure. Soil structure was assessed using a visual rating. Soil resistance measurements were taken over a range of soil wetness, using a recording penetrometer. Readings were taken as the soil dried by evapotranspiration after both irrigation and rainfall events.
The influence of soil wetness on penetration resistance was greater on fields with degraded structure than on well-structured fields. In fields with degraded structure, the wetter the soil, the smaller were the penetration resistance values. Field soil structure score was negatively correlated with the slope of the line relating soil wetness and penetration resistance at 150–300 mm depth. The structurally degraded fields had a highly significant relationship between penetration resistance and soil wetness at 150–300 mm depth. In well-structured fields, variations in soil wetness had less effect on penetration resistance.
These results indicate that visual assessment can be used with confidence to assess Ferrosol structure. The implications for soil management are that fields with degraded soil structure have greater resistance to root growth at drier moisture contents than well-structured fields. Consequently, farmers need to keep degraded soils wetter with more frequent irrigation than well-structured soils, to ensure optimum plant growth.
Oxygen transport in soil and the vertical distribution of roots
Authors: Cook F. J. , Knight J. H. , Kelliher F. M.
Published: March 2007

An analytical solution for steady-state oxygen transport in soils including 2 sink terms, viz roots and microbes with the corresponding vertical distribution scaling lengths forming a ratio p, showed p governed the critical air-filled porosity, θc, needed by most plants. For low temperature and p, θc was <0.1 but at higher temperatures and p = 1, θc was >0.15 m3/m3. When root length density at the surface was 104 m/m3 and p > 3, θc was 0.25 m3/m3, more than half the pore space. Few combinations of soil and climate regularly meet this condition. However, for sandy soils and seasonally warm, arid regions, the theory is consistent with observation, in that plants may have some deep roots. Critical θc values are used to formulate theoretical solutions in a forward mode, so different levels of oxygen uptake by roots may be compared to microbial activity. The proportion of respiration by plant roots increases rapidly with p up to p ≈2.
Synthesis of vertical root biomass density, L [= L0 exp(–z/Zr), z is the depth positive down (m)] (m/m3), data using an exponential function to represent the distribution suggested that, on average, 70 ± 10% of fine roots in 10 terrestrial biomes were located in the upper 0.1 m of soil. Integrated over the root-zone, LT is given by the product of the function’s 2 parameters, the surface value of L, L0 (m/m3), and length scale, Zr (m). As postulated, negative correlations were obtained between L0 and Zr. For a maize (Zea mays L.) crop, significantly different distributions were measured during relatively dry and wet seasons and predicted by our model. For woody and herbaceous plants, Zr (the value determines the rate of decrease in L with depth) averaged 0.3 and 0.2 m, respectively, while the corresponding averages for Rm0 [= L0.ρr, ρr is root density (kg/m)] were 2.7 and 1.1 kg/m3.
Cytosolic phospholipase A
2
alpha mediates electrophysiologic responses of hippocampal pyramidal neurons to neurotoxic NMDA treatment
Authors: Shen Ying , Kishimoto Koji , Linden David J. , Sapirstein Adam
Published: March 2007

The arachidonic acid-generating enzyme cytosolic phospholipase A
2
alpha (cPLA
2
α) has been implicated in the progression of excitotoxic neuronal injury. However, the mechanisms of cPLA
2
α toxicity have yet to be determined. Here, we used a model system exposing mouse hippocampal slices to NMDA as an excitotoxic injury, in combination with simultaneous patch-clamp recording and confocal Ca
2+
imaging of CA1 pyramidal neurons. NMDA treatment caused significantly greater injury in wild-type (WT) than in cPLA
2
α null CA1 neurons. Bath application of NMDA evoked a slow inward current in voltage-clamped neurons (composed of both NMDA receptor-mediated and other conductances) that was smaller in cPLA
2
α null than in WT slices. This was not due to down-regulation of NMDA receptor function because NMDA receptor-mediated currents were equivalent in each genotype following brief photolysis of caged glutamate. Current-clamp recordings were made during and following NMDA exposure by eliciting a single action potential with a brief current injection. After NMDA exposure, WT CA1 neurons developed a spike-evoked plateau potential and an increased spike-evoked dendritic Ca
2+
transient. These effects were absent in CA1 neurons from cPLA
2
α null mice and WT neurons treated with a cPLA
2
α inhibitor. The Ca-sensitive K-channel toxins, apamin and paxilline, caused spike broadening and Ca
2+
enhancement in WT and cPLA
2
α null slices. NMDA application in WT and arachidonate applied to cPLA
2
α null cells occluded the effects of apamin/paxilline. These results indicate that cPLA
2
α activity is required for development of aberrant electrophysiologic events triggered by NMDA receptor activation, in part through attenuation of K-channel function.
Projected distributions of novel and disappearing climates by 2100 AD
Authors: Williams John W. , Jackson Stephen T. , Kutzbach John E.
Published: March 2007

Key risks associated with projected climate trends for the 21st century include the prospects of future climate states with no current analog and the disappearance of some extant climates. Because climate is a primary control on species distributions and ecosystem processes, novel 21st-century climates may promote formation of novel species associations and other ecological surprises, whereas the disappearance of some extant climates increases risk of extinction for species with narrow geographic or climatic distributions and disruption of existing communities. Here we analyze multimodel ensembles for the A2 and B1 emission scenarios produced for the fourth assessment report of the Intergovernmental Panel on Climate Change, with the goal of identifying regions projected to experience (
i
) high magnitudes of local climate change, (
ii
) development of novel 21st-century climates, and/or (
iii
) the disappearance of extant climates. Novel climates are projected to develop primarily in the tropics and subtropics, whereas disappearing climates are concentrated in tropical montane regions and the poleward portions of continents. Under the high-end A2 scenario, 12–39% and 10–48% of the Earth's terrestrial surface may respectively experience novel and disappearing climates by 2100 AD. Corresponding projections for the low-end B1 scenario are 4–20% and 4–20%. Dispersal limitations increase the risk that species will experience the loss of extant climates or the occurrence of novel climates. There is a close correspondence between regions with globally disappearing climates and previously identified biodiversity hotspots; for these regions, standard conservation solutions (e.g., assisted migration and networked reserves) may be insufficient to preserve biodiversity.
Coordinate expression and functional profiling identify an extracellular proteolytic signaling pathway
Authors: Bhatt Ami S. , Welm Alana , Farady Christopher J. , Vásquez Maximiliano , Wilson Keith , Craik Charles S.
Published: March 2007

A multidisciplinary method combining transcriptional data, specificity profiling, and biological characterization of an enzyme may be used to predict novel substrates. By integrating protease substrate profiling with microarray gene coexpression data from nearly 2,000 human normal and cancerous tissue samples, three fundamental components of a protease-activated signaling pathway were identified. We find that MT-SP1 mediates extracellular signaling by regulating the local activation of the prometastatic growth factor MSP-1. We demonstrate MT-SP1 expression in peritoneal macrophages, and biochemical methods confirm the ability of MT-SP1 to cleave and activate pro-MSP-1in vitroand in a cellular context. MT-SP1 induced the ability of MSP-1 to inhibit nitric oxide production in bone marrow macrophages. Addition of HAI-1 or an MT-SP1-specific antibody inhibitor blocked the proteolytic activation of MSP-1 at the cell surface of peritoneal macrophages. Taken together, our work indicates that MT-SP1 is sufficient for MSP-1 activation and that MT-SP1, MSP-1, and the previously shown MSP-1 tyrosine kinase receptor RON are required for peritoneal macrophage activation. This work shows that this triad of growth factor, growth factor activator protease, and growth factor receptor is a protease-activated signaling pathway. Individually, MT-SP1 and RON overexpression have been implicated in cancer progression and metastasis. Transcriptional coexpression of these genes suggests that this signaling pathway may be involved in several human cancers.
Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex
Authors: Gilbert Robert J. C. , Gordiyenko Yulya , von der Haar Tobias , Sonnen Andreas F.-P. , Hofmann Gregor , Nardelli Maria , Stuart David I. , McCarthy John E. G.
Published: March 2007

In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5′ end of the mRNA, from which point it scans along the 5′ untranslated region in search of a start codon. However, the 40S subunit alone is not capable of functional association with cellular mRNA species; it has to be prepared for the recruitment and scanning steps by interactions with a group of eukaryotic initiation factors (eIFs). In budding yeast, an important subset of these factors (
1
,
2
,
3
, and
5
) can form a multifactor complex (MFC). Here, we describe cryo-EM reconstructions of the 40S subunit, of the MFC, and of 40S complexes with MFC factors plus eIF1A. These studies reveal the positioning of the core MFC on the 40S subunit, and show how eIF-binding induces mobility in the head and platform and reconfigures the head–platform–body relationship. This is expected to increase the accessibility of the mRNA channel, thus enabling the 40S subunit to convert to a recruitment-competent state.
Crucial roles ofFoxa2in mouse anterior–posterior axis polarization via regulation of anterior visceral endoderm-specific genes
Authors: Kimura-Yoshida Chiharu , Tian E. , Nakano Hiroshi , Amazaki Saori , Shimokawa Kayo , Rossant Janet , Aizawa Shinichi , Matsuo Isao
Published: March 2007

Anterior visceral endoderm (AVE) plays essential roles with respect to anterior–posterior axis development in the early mouse embryo. To assess the genetic cascade involved in AVE formation, the cis-regulatory elements directing expression of vertebrateOtx2genes in the AVE were analyzed via generation of transgenic mice.Otx2expression in AVE is regulated directly by the forkhead transcription factor,Foxa2. Moreover,Foxa2is essential for expression of theWntantagonists,Dkk1andCerl, in visceral endoderm during the pre- to early streak stages; however,Foxa2appears to be dispensable for subsequentDkk1expression associated with forebrain induction. Thus, we propose thatFoxa2is crucial in early anterior–posterior axis polarization in terms of regulation of expression of AVE-specific genes. These findings provide profound insights into conserved roles ofFoxa2transcription factors in anterior specification throughout the evolution of the chordate body plan.
CCR4/NOT complex associates with the proteasome and regulates histone methylation
Authors: Laribee R. Nicholas , Shibata Yoichiro , Mersman Douglas P. , Collins Sean R. , Kemmeren Patrick , Roguev Assen , Weissman Jonathan S. , Briggs Scott D. , Krogan Nevan J. , Strahl Brian D.
Published: March 2007

The proteasome regulates histone lysine methylation and gene transcription, but how it does so is poorly understood. To better understand this process, we used the epistatic miniarray profile (E-MAP) approach to identify factors that genetically interact with proteasomal subunits. In addition to members of the Set1 complex that mediate histone H3 lysine 4 methylation (H3K4me), we found that deleting members of the CCR4/NOT mRNA processing complex exhibit synthetic phenotypes when combined with proteasome mutants. Further biochemical analyses revealed physical associations between CCR4/NOT and the proteasome
in vivo
. Consistent with the genetic and biochemical interactions linking CCR4/NOT with proteasome and Set1-mediated methylation, we find that loss of Not4 decreases global and gene-specific H3K4 trimethylation (H3K4me3) and decreases 19S proteasome recruitment to the
PMA1
gene. Similar to proteasome regulation of histone methylation, loss of CCR4/NOT members does not affect ubiquitinated H2B. Mapping of Not4 identified the RING finger domain as essential for H3K4me3, suggesting a role for ubiquitin in this process. Consistent with this idea, loss of the Not4-interacting protein Ubc4, a known ubiquitin-conjugating enzyme, decreases H3K4me3. These studies implicate CCR4/NOT in the regulation of H3K4me3 through a ubiquitin-dependent pathway that likely involves the proteasome.
Coarse-grained analysis of stochasticity-induced switching between collective motion states
Authors: Kolpas Allison , Moehlis Jeff , Kevrekidis Ioannis G.
Published: March 2007

A single animal group can display different types of collective motion at different times. For a one-dimensional individual-based model of self-organizing group formation, we show that repeated switching between distinct ordered collective states can occur entirely because of stochastic effects. We introduce a framework for the coarse-grained, computer-assisted analysis of such stochasticity-induced switching in animal groups. This involves the characterization of the behavior of the system with a single dynamically meaningful “coarse observable” whose dynamics are described by an effective Fokker–Planck equation. A “lifting” procedure is presented, which enables efficient estimation of the necessary macroscopic quantities for this description through short bursts of appropriately initialized computations. This leads to the construction of an effective potential, which is used to locate metastable collective states, and their parametric dependence, as well as estimate mean switching times.
Micromechanical control of cell–cell interactions
Authors: Hui Elliot E. , Bhatia Sangeeta N.
Published: March 2007

The development and function of living tissues depends largely on interactions between cells that can vary in both time and space; however, temporal control of cell–cell interaction is experimentally challenging. By using a micromachined silicon substrate with moving parts, we demonstrate the dynamic regulation of cell–cell interactions via direct manipulation of adherent cells with micrometer-scale precision. We thereby achieve mechanical control of both tissue composition and spatial organization. As a case study, we demonstrate the utility of this tool in deconstructing the dynamics of intercellular communication between hepatocytes and supportive stromal cells in coculture. Our findings indicate that the maintenance of the hepatocellular phenotype by stroma requires direct contact for a limited time (≈hours) followed by a sustained soluble signal that has an effective range of <400 μm. This platform enables investigation of dynamic cell–cell interaction in a multitude of applications, spanning embryogenesis, homeostasis, and pathogenic processes.
Abscisic acid is an endogenous cytokine in human granulocytes with cyclic ADP-ribose as second messenger
Authors: Bruzzone Santina , Moreschi Iliana , Usai Cesare , Guida Lucrezia , Damonte Gianluca , Salis Annalisa , Scarfì Sonia , Millo Enrico , De Flora Antonio , Zocchi Elena
Published: March 2007

Abscisic acid (ABA) is a phytohormone involved in fundamental physiological processes of higher plants, such as response to abiotic stress (temperature, light, drought), regulation of seed dormancy and germination, and control of stomatal closure. Here, we provide evidence that ABA stimulates several functional activities [phagocytosis, reactive oxygen species and nitric oxide (NO) production, and chemotaxis] of human granulocytes through a signaling pathway sequentially involving a pertussis toxin (PTX)-sensitive G protein/receptor complex, protein kinase A activation, ADP-ribosyl cyclase phosphorylation, and consequent cyclic-ADP-ribose overproduction, leading to an increase of the intracellular Ca
2+
concentration. The increase of free intracellular ABA and its release by activated human granulocytes indicate that ABA should be considered as a new pro-inflammatory cytokine in humans. This discovery is an intriguing example of conservation of a hormone and its signaling pathway from plants to humans and provides insight into the molecular mechanisms of granulocyte activation, possibly leading to the development of new antiinflammatory drugs.
Genomic imprinting mediates sexual experience-dependent olfactory learning in male mice
Authors: Swaney William T. , Curley James P. , Champagne Frances A. , Keverne Eric B.
Published: March 2007

Mammalian imprinted genes are generally thought to have evolved as a result of conflict between parents; however, recent knockout studies suggest that coadaptation between mother and offspring may have been a significant factor. We present evidence that the same imprinted gene that regulates mammalian maternal care and offspring development also regulates male sexual behavior and olfaction. We have shown that the behavior of male mice carrying a knockout of the imprinted gene
Peg3
does not change with sexual experience and that the mice are consequently unable to improve their copulatory abilities or olfactory interest in female odor cues after mating experience. Forebrain activation, as indexed by female odor-induced c-Fos protein induction, fails to increase with sexual experience, providing a neural basis for the behavioral deficits that the male mice display. The behavioral and neural effects of the
Peg3
knockout show that this imprinted gene has evolved to regulate multiple and varied aspects of reproduction, from male sexual behavior to female maternal care, and the development of offspring. Moreover, sexual experience-driven behavioral changes may represent an adaptive response that enables males to increase their reproductive potential over their lifespan, and the effects we have found suggest that the evolution of genomic imprinting has been influenced by coadaptation between males and females as well as between females and offspring.
In vivo
negative selection screen identifies genes required for
Francisella
virulence
Authors: Weiss David S. , Brotcke Anna , Henry Thomas , Margolis Jeffrey J. , Chan Kaman , Monack Denise M.
Published: March 2007

Francisella tularensis
subverts the immune system to rapidly grow within mammalian hosts, often causing tularemia, a fatal disease. This pathogen targets the cytosol of macrophages where it replicates by using the genes encoded in the
Francisella
pathogenicity island. However, the bacteria are recognized in the cytosol by the host's ASC/caspase-1 pathway, which is essential for host defense, and leads to macrophage cell death and proinflammatory cytokine production. We used a microarray-based negative selection screen to identify
Francisella
genes that contribute to growth and/or survival in mice. The screen identified many known virulence factors including all of the
Francisella
pathogenicity island genes, LPS O-antigen synthetic genes, and capsule synthetic genes. We also identified 44 previously unidentified genes that were required for
Francisella
virulence
in vivo
, indicating that this pathogen may use uncharacterized mechanisms to cause disease. Among these, we discovered a class of
Francisella
virulence genes that are essential for growth and survival
in vivo
but do not play a role in intracellular replication within macrophages. Instead, these genes modulate the host ASC/caspase-1 pathway, a previously unidentified mechanism of
Francisella
pathogenesis. This finding indicates that the elucidation of the molecular mechanisms used by other uncharacterized genes identified in our screen will increase our understanding of the ways in which bacterial pathogens subvert the immune system.
Riboflavin activated by ultraviolet A1 irradiation induces oxidative DNA damage-mediated mutations inhibited by vitamin C
Authors: Besaratinia Ahmad , Kim Sang-in , Bates Steven E. , Pfeifer Gerd P.
Published: March 2007

An increasingly popular theory ascribes UVA (>320–400 nm) carcinogenicity to the ability of this wavelength to trigger intracellular photosensitization reactions, thereby giving rise to promutagenic oxidative DNA damage. We have tested this theory both at the genomic and nucleotide resolution level in mouse embryonic fibroblasts carrying the lambda phage
cII
transgene. We have also tested the hypothesis that inclusion of a cellular photosensitizer (riboflavin) can intensify UVA-induced DNA damage and mutagenesis, whereas addition of an antioxidant (vitamin C) can counteract the induced effects. Cleavage assays with formamidopyrimidine DNA glycosylase (Fpg) coupled to alkaline gel electrophoresis and ligation-mediated PCR (LM-PCR) showed that riboflavin treatment (1 μM) combined with UVA1 (340–400 nm) irradiation (7.68 J/cm
2
) or higher dose UVA1 irradiation alone induced Fpg-sensitive sites (indicative of oxidized and/or ring-opened purines) in the overall genome and in the
cII
transgene, respectively. Also, the combined treatment with riboflavin and UVA1 irradiation gave rise to single-strand DNA breaks in the genome and in the
cII
transgene determined by terminal transferase-dependent PCR (TD-PCR). A cotreatment with vitamin C (1 mM) efficiently inhibited the formation of the induced lesions. Mutagenicity analysis showed that riboflavin treatment combined with UVA1 irradiation or high-dose UVA1 irradiation alone significantly increased the relative frequency of
cII
mutants, both mutation spectra exhibiting significant increases in the relative frequency of G:C → T:A transversions, the signature mutations of oxidative DNA damage. The induction of
cII
mutant frequency was effectively reduced consequent to a cotreatment with vitamin C. Our findings support the notion that UVA-induced photosensitization reactions are responsible for oxidative DNA damage leading to mutagenesis.
The role of pannexin 1 hemichannels in ATP release and cell–cell communication in mouse taste buds
Authors: Huang Yi-Jen , Maruyama Yutaka , Dvoryanchikov Gennady , Pereira Elizabeth , Chaudhari Nirupa , Roper Stephen D.
Published: March 2007

ATP has been shown to be a taste bud afferent transmitter, but the cells responsible for, and the mechanism of, its release have not been identified. Using CHO cells expressing high-affinity neurotransmitter receptors as biosensors, we show that gustatory stimuli cause receptor cells to secrete ATP through pannexin 1 hemichannels in mouse taste buds. ATP further stimulates other taste cells to release a second transmitter, serotonin. These results provide a mechanism to link intracellular Ca
2+
release during taste transduction to secretion of afferent transmitter, ATP, from receptor cells. They also indicate a route for cell–cell communication and signal processing within the taste bud.
Structural insight into substrate specificity of phosphodiesterase 10
Authors: Wang Huanchen , Liu Yudong , Hou Jing , Zheng Meiyan , Robinson Howard , Ke Hengming
Published: March 2007

Phosphodiesterases (PDEs) hydrolyze the second messengers cAMP and cGMP. It remains unknown how individual PDE families selectively recognize cAMP and cGMP. This work reports structural studies on substrate specificity. The crystal structures of the catalytic domains of the D674A and D564N mutants of PDE10A2 in complex with cAMP and cGMP reveal that two substrates bind to the active site with the samesynconfiguration but different orientations and interactions. The products AMP and GMP bind PDE10A2 with theanticonfiguration and interact with both divalent metals, in contrast to no direct contact of the substrates. The structures suggest that thesynconfigurations of cAMP and cGMP are the genuine substrates for PDE10 and the specificity is achieved through the different interactions and conformations of the substrates. The PDE10A2 structures also show that the conformation of the invariant glutamine is locked by two hydrogen bonds and is unlikely to switch for substrate recognition. Sequence alignment shows a potential pocket, in which variation of amino acids across PDE families defines the size and shape of the pocket and thus determines the substrate specificity.
Naloxone acts as a potent analgesic in transgenic mouse models of sickle cell anemia
Authors: Lunzer Mary M. , Yekkirala Ajay , Hebbel Robert P. , Portoghese Philip S.
Published: March 2007

Sickle cell anemia is a common genetic disorder in African Americans. Opioid analgesics are traditionally the treatment for the severe pain associated with this disease. Here we reveal that the opioid antagonist naloxone possesses potent analgesic activity in two transgenic mouse models of sickle cell anemia (NY1DD and hBERK1) and not in their respective controls (ICR-CD1 and C57BL/6J) when administered by three parenteral routes [intracerebroventricular (i.c.v.), intrathecal, and subcutaneous]. In the NY1DD mice, naloxone (i.c.v.) possessed ≈300-fold greater potency than morphine (i.c.v.). Other opioid antagonists (naltrexone, norbinaltorphimine, and naltrindole) were substantially less effective in producing analgesia. Naloxone and morphine were synergistic in NY1DD mice, suggesting different receptor systems. Microarray analysis suggested naloxone-induced down-regulation of the CC chemokine receptor (CCR)5 in NY1DD mice but not in control mice. Pretreatment of control mice with CC chemokine ligand 5 [CCL5 (RANTES)] enabled naloxone to produce analgesia similar to that observed in NY1DD mice. Mu opioid receptor knockout mice treated similarly also displayed analgesia. That the effect of CCL5 was specifically related to CCR5 and/or CCR1 activation was demonstrated by antagonism of analgesia with the chemokine antagonist methionylated RANTES. Similar antagonism of naloxone-induced analgesia also was observed when NY1DD mice were pretreated with methionylated RANTES. These results indicate that CCR5/CCR1 receptors are directly or indirectly involved in analgesia produced by naloxone. The present study suggests that naloxone may be clinically useful in the treatment of pain associated with sickle cell disease and other disorders involving inflammation.
Morlin, an inhibitor of cortical microtubule dynamics and cellulose synthase movement
Authors: DeBolt Seth , Gutierrez Ryan , Ehrhardt David W. , Melo Carlos V. , Ross Loretta , Cutler Sean R. , Somerville Christopher , Bonetta Dario
Published: March 2007

Morlin (7-ethoxy-4-methyl chromen-2-one) was discovered in a screen of 20,000 compounds for small molecules that cause altered cell morphology resulting in swollen root phenotype in
Arabidopsis
. Live-cell imaging of fluorescently labeled cellulose synthase (CESA) and microtubules showed that morlin acts on the cortical microtubules and alters the movement of CESA. Morlin caused a novel syndrome of cytoskeletal defects, characterized by cortical array reorientation and compromised rates of both microtubule elongation and shrinking. Formation of shorter and more bundled microtubules and detachment from the cell membrane resulted when GFP::MAP4-MBP was used to visualize microtubules during morlin treatment. Cytoskeletal effects were accompanied by a reduction in the velocity and redistribution of CESA complexes labeled with YFP::CESA6 at the cell cortex. Morlin caused no inhibition of mouse myoblast, bacterial or fungal cell proliferation at concentrations that inhibit plant cell growth. By contrast, morlin stimulated microtubule disassembly in cultured hippocampal neurons but had no significant effect on cell viability. Thus, morlin appears to be a useful new probe of the mechanisms that regulate microtubule cortical array organization and its functional interaction with CESA.
Costimulatory ligand CD70 is delivered to the immunological synapse by shared intracellular trafficking with MHC class II molecules
Authors: Keller Anna M. , Groothuis Tom A. , Veraar Elise A. M. , Marsman Marije , de Buy Wenniger Lucas Maillette , Janssen Hans , Neefjes Jacques , Borst Jannie
Published: March 2007

TNF family member CD70 is the ligand of CD27, a costimulatory receptor that shapes effector and memory T cell pools. Tight control of CD70 expression is required to prevent lethal immunodeficiency. By selective transcription, CD70 is largely confined to activated lymphocytes and dendritic cells (DC). We show here that, in addition, specific intracellular routing controls its plasma membrane deposition. In professional antigen-presenting cells, such as DC, CD70 is sorted to late endocytic vesicles, defined as MHC class II compartments (MIIC). In cells lacking the machinery for antigen presentation by MHC class II, CD70 travels by default to the plasma membrane. Introduction of class II transactivator sufficed to reroute CD70 to MIIC. Vesicular trafficking of CD70 and MHC class II is coordinately regulated by the microtubule-associated dynein motor complex. We show that when maturing DC make contact with T cells in a cognate fashion, newly synthesized CD70 is specifically delivered via MIIC to the immunological synapse. Therefore, we propose that routing of CD70 to MIIC serves to coordinate delivery of the T cell costimulatory signal in time and space with antigen recognition.
A coupled geomorphic and ecological model of tidal marsh evolution
Authors: Kirwan Matthew L. , Murray A. Brad
Published: March 2007

The evolution of tidal marsh platforms and interwoven channel networks cannot be addressed without treating the two-way interactions that link biological and physical processes. We have developed a 3D model of tidal marsh accretion and channel network development that couples physical sediment transport processes with vegetation biomass productivity. Tidal flow tends to cause erosion, whereas vegetation biomass, a function of bed surface depth below high tide, influences the rate of sediment deposition and slope-driven transport processes such as creek bank slumping. With a steady, moderate rise in sea level, the model builds a marsh platform and channel network with accretion rates everywhere equal to the rate of sea-level rise, meaning water depths and biological productivity remain temporally constant. An increase in the rate of sea-level rise, or a reduction in sediment supply, causes marsh-surface depths, biomass productivity, and deposition rates to increase while simultaneously causing the channel network to expand. Vegetation on the marsh platform can promote a metastable equilibrium where the platform maintains elevation relative to a rapidly rising sea level, although disturbance to vegetation could cause irreversible loss of marsh habitat.
Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
Authors: Takahashi Mihoko , Kondou Youhei , Toyoshima Chikashi
Published: March 2007

Ca
2+
-ATPase of skeletal muscle sarcoplasmic reticulum is an ATP-driven Ca
2+
pump consisting of three cytoplasmic domains and 10 transmembrane helices. In the absence of Ca
2+
, the three cytoplasmic domains gather to form a compact headpiece, but the ATPase is unstable without an inhibitor. Here we describe the crystal structures of Ca
2+
-ATPase in the absence of Ca
2+
stabilized with cyclopiazonic acid alone and in combination with other inhibitors. Cyclopiazonic acid is located in the transmembrane region of the protein near the cytoplasmic surface. The binding site partially overlaps with that of 2,5-di-
tert
-butyl-1,4-dihydroxybenzene but is separate from that of thapsigargin. The overall structure is significantly different from that stabilized with thapsigargin: The cytoplasmic headpiece is more upright, and the transmembrane helices M1–M4 are rearranged. Cyclopiazonic acid primarily alters the position of the M1′ helix and thereby M2 and M4 and then M5. Because M5 is integrated into the phosphorylation domain, the whole cytoplasmic headpiece moves. These structural changes show how an event in the transmembrane domain can be transmitted to the cytoplasmic domain despite flexible links between them. They also reveal that Ca
2+
-ATPase has considerable plasticity even when fixed by a transmembrane inhibitor, presumably to accommodate thermal fluctuations.
Metagene projection for cross-platform, cross-species characterization of global transcriptional states
Authors: Tamayo Pablo , Scanfeld Daniel , Ebert Benjamin L. , Gillette Michael A. , Roberts Charles W. M. , Mesirov Jill P.
Published: March 2007

The high dimensionality of global transcription profiles, the expression level of 20,000 genes in a much small number of samples, presents challenges that affect the sensitivity and general applicability of analysis results. In principle, it would be better to describe the data in terms of a small number of metagenes, positive linear combinations of genes, which could reduce noise while still capturing the invariant biological features of the data. Here, we describe how to accomplish such a reduction in dimension by a metagene projection methodology, which can greatly reduce the number of features used to characterize microarray data. We show, in applications to the analysis of leukemia and lung cancer data sets, how this approach can help assess and interpret similarities and differences between independent data sets, enable cross-platform and cross-species analysis, improve clustering and class prediction, and provide a computational means to detect and remove sample contamination.
Neural encoding of the concept of nest in the mouse brain
Authors: Lin Longnian , Chen Guifen , Kuang Hui , Wang Dong , Tsien Joe Z.
Published: March 2007

As important as memory is to our daily functions, the ability to extract fundamental features and commonalities from various episodic experiences and to then generalize them into abstract concepts is even more crucial for both humans and animals to adapt to novel and complex situations. Here, we report the neural correlates of the abstract concept of nests or beds in mice. Specifically, we find hippocampal neurons that selectively fire or cease to fire when the mouse perceives nests or beds, regardless of their locations and environments. Parametric analyses show that responses of nest cells remain invariant over changes in the nests' physical shape, style, color, odor, or construction materials; rather, their responses are driven by conscious awareness and physical determination of the categorical features that would functionally define nests. Such functionality-based abstraction and generalization of conceptual knowledge, emerging from episodic experiences, suggests that the hippocampus is an intrinsic part of the hierarchical structure for generating concepts and knowledge in the brain.
Destruction of long-range interactions by a single mutation in lysozyme
Authors: Zhou Ruhong , Eleftheriou Maria , Royyuru Ajay K. , Berne Bruce J.
Published: March 2007

We propose a mechanism, based on a ≥10-μs molecular dynamics simulation, for the surprising misfolding of hen egg-white lysozyme caused by a single mutation (W62G). Our simulations of the wild-type and mutant lysozymes in 8 M urea solution at biological temperature (with both pH 2 and 7) reveal that the mutant structure is much less stable than that of the wild type, with the mutant showing larger fluctuations and less native-like contacts. Analysis of local contacts reveals that the Trp-62 residue is the key to a cooperative long-range interaction within the wild type, where it acts like a bridge between two neighboring basic residues. Thus, a native-like cluster or nucleation site can form near these residues in the wild type but not in the mutant. The time evolution of the secondary structure also exhibits a quicker loss of the β-sheets in the mutant than in the wild type, whereas some of the α-helices persist during the entire simulation in both the wild type and the mutant in 8 M urea (even though the tertiary structures are basically all gone). These findings, while supporting the general conclusions of a recent experimental study by Dobson and coworkers [Klein-Seetharam J, Oikama M, Grimshaw SB, Wirmer J, Duchardt E, Ueda T, Imoto T, Smith LJ, Dobson CM, Schwalbe H (2002)
Science
295:1719–1722], provide a detailed but different molecular picture of the misfolding mechanism.
Structural insights into the degradation of Mcl-1 induced by BH3 domains
Authors: Czabotar Peter E. , Lee Erinna F. , van Delft Mark F. , Day Catherine L. , Smith Brian J. , Huang David C. S. , Fairlie W. Douglas , Hinds Mark G. , Colman Peter M.
Published: March 2007

Apoptosis is held in check by prosurvival proteins of the Bcl-2 family. The distantly related BH3-only proteins bind to and antagonize them, thereby promoting apoptosis. Whereas binding of the BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1 degradation by the proteasome, binding of another BH3-only ligand, Bim, elevates Mcl-1 protein levels. We compared the three-dimensional structures of the complexes formed between BH3 peptides of both Bim and Noxa, and we show that a discrete C-terminal sequence of the Noxa BH3 is necessary to instigate Mcl-1 degradation.