bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of the last glacial inception with the green McGill Paleoclimate Model
Authors: Wang Zhaomin , Cochelin Anne‐Sophie B. , Mysak Lawrence A. , Wang Yi
Published: June 2005

The “green” McGill Paleoclimate Model (MPM), which includes an interactive vegetation component, is run between 122 and 80 kyr Before Present (BP) under Milankovitch forcing and Vostok‐derived atmospheric CO2 concentration. The model simulates the last glacial inception (LGI) at around 119 kyr BP, and the subsequent buildup of huge ice sheets over the high northern latitudes, especially North America. Due to the addition of a vegetation component and an improved land surface scheme in the MPM, the resulting ice sheet volume is relatively small over Eurasia but quite large over North America, which is in qualitative agreement with observations and represents a significant improvement over the LGI results from the previous version of the MPM. The reduction of the forest area at high northern latitudes during the inception phase, which is induced by decreased warm season insolation, is necessary for the ice sheets to grow over Eurasia and to have large ice sheet growth over North America.
Modeling the influence of Moho topography on receiver functions: A case study from the central Hellenic subduction zone
Authors: Endrun B. , Ceranna L. , Meier T. , Bohnhoff M. , Harjes H.‐P.
Published: June 2005

Pseudospectral 2D modeling of wave propagation provides a fresh look at receiver function data from the Hellenic subduction zone. It is shown that distinct Moho topography, which is suggested for this complex subduction environment from various geophysical data sets, can provide a conclusive explanation for previously observed “inverted” Moho phases in the forearc as well as for a complex sequence of apparently dipping conversions in the volcanic arc. Prominent effects of strongly dipping discontinuities include the change of sign in Ps phases refracted past the vertical and multiple P reflections that cannot be separated from Ps conversions during receiver function processing. Unambiguous identification of these phenomena can be hampered by poor azimuthal coverage of the data. Still, in regions where discontinuity topography can reasonably be expected, its effects should be considered when interpreting receiver functions, as results might be spurious otherwise.
Titan's ionosphere: Model comparisons with Cassini Ta data
Authors: Cravens T. E. , Robertson I. P. , Clark J. , Wahlund J.‐E. , Waite J. H. , Ledvina S. A. , Niemann H. B. , Yelle R. V. , Kasprzak W. T. , Luhmann J. G. , McNutt R. L. , Ip W.‐H. , De La Haye V. , Müller‐Wodarg I. , Young D. T. , Coates A. J.
Published: June 2005

On October 26, 2004, during its first encounter with Titan (Ta), the Cassini Orbiter moved from the dayside to the nightside with a closest approach altitude of 1174 km. In situ measurements of the main part of Titan's ionosphere were made by the Langmuir probe on the Cassini Radio and Plasma Wave Experiment (RPWS), while the Ion and Neutral Mass Spectrometer (INMS) measured the main constituents of the neutral atmosphere. The results of model calculations of Titan's ionosphere for Ta encounter conditions (e.g., near the terminator) are presented in this paper. The paper includes comparisons of calculated and measured electron densities along the spacecraft track. Ionization both by solar radiation and by incoming energetic electrons from Saturn's magnetosphere are needed to obtain good agreement between the measured and calculated electron densities.
Intra-specific variation in leaf attributes of four savanna tree species across a rainfall gradient in tropical Australia
Authors: Prior L. D. , Bowman D. M. J. S. , Eamus D.
Published: June 2005

Leaf attributes of four savanna tree species were measured along a rainfall gradient (1650–950 mm per annum) in the Australian monsoon tropics. As the mean annual rainfall decreased, leaf thickness increased for three of these four species. However, a corresponding decrease in leaf density for two species meant that leaf mass per area increased significantly only for one species. Physiological measurements were made during both the wet and dry seasons on comparable stands of vegetation near the extremes and middle of this gradient. Assimilation per unit mass was similar at all three sites but assimilation per leaf area was higher at the drier sites because leaves were thicker with higher mass per area. These results probably reflect reduced tree density and leaf area index at the drier sites, which offsets the lower rainfall, potentially allowing similar rates of assimilation per unit carbohydrate invested in leaves.
Outcrossing in interspecific hybrids between Eucalyptus spathulata and E. platypus
Authors: Wallwork M. A. B. , Sedgley M.
Published: June 2005

Outcrossing was investigated in interspecific hybrids between self-fertile Eucalyptus platypus Blakely and partially self-sterile E. spathulata Hook., which shows both pre- and post-zygotic timing. Four hybrid trees were used for the study, two with E. spathulata and two with E. platypus as female parent. Each hybrid had a similar number of locules to each other and to the E. platypus parent, and an intermediate number of ovules per flower compared with the parent species. Controlled hand-pollinations were carried out, in which both self- and cross-pollen from the other hybrid tree with the same female parent species was applied to flowers on each of the four trees, and observations were made 10days, 4weeks and 8weeks after pollination and at seed maturity. In all hybrids, mean seeds per capsule was consistently higher following cross-pollination than following self-pollination. All hybrids showed a reduction in pollen tube number between the top and base of the style when examined by fluorescence microscopy. One tree had significantly fewer cross- than self-pollen tubes at the base of the style, but a similar number of ovules was penetrated by pollen tubes following both treatments. In the other three, there was no difference between cross- and self-pollination in pollen tubes in the style. In three of the four trees there was no difference in ovule penetration following self- or cross-pollination, but in the other, more crossed than selfed ovules were penetrated. Light-microscopy observation of ovules indicated that ovule abortion following fertilisation accounted for the reduced numbers of seeds following self-pollination and to a lesser extent following cross-pollination. All four hybrid trees, irrespective of female parent, were partially self-sterile and resembled the partially self-sterile E. spathulata rather than the self-fertile E. platypus. While the timing of outcrossing control of E. spathulata was both pre- and post-zygotic, only one hybrid was similar, with the other three showing post-zygotic control.
Classifying Eucalyptus forests with high spatial and spectral resolution imagery: an investigation of individual species and vegetation communities
Authors: Goodwin Nicholas , Turner Russell , Merton Ray
Published: June 2005

Mapping the spatial distribution of individual species is an important ecological and forestry issue that requires continued research to coincide with advances in remote-sensing technologies. In this study, we investigated the application of high spatial resolution (80 cm) Compact Airborne Spectrographic Imager 2 (CASI-2) data for mapping both spectrally complex species and species groups (subgenus grouping) in an Australian eucalypt forest. The relationships between spectral reflectance curves of individual tree species and identified statistical differences among species were analysed with ANOVA. Supervised maximum likelihood classifications were then performed to assess tree species separability in CASI-2 imagery. Results indicated that turpentine (Syncarpia glomulifera Smith), mesic vegetation (primarily rainforest species), and an amalgamated group of eucalypts could be readily distinguished. The discrimination of S. glomulifera was particularly robust, with consistently high classification accuracies. Eucalypt classification as a broader species group, rather than individual species, greatly improved classification performance. However, separating sunlit and shaded aspects of tree crowns did not increase classification accuracy.
Breeding system of Tristerix corymbosus (Loranthaceae), a winter-flowering mistletoe from the southern Andes
Authors: Aizen Marcelo A.
Published: June 2005

Harsh climates should select for breeding systems that uncouple reproductive success from unpredictable pollinator service, such as autonomous, within-flower pollination and autogamous seed set. I assessed the breeding system and overall pollinator dependence of Tristerix corymbosus (L.) Kuijt, a mistletoe that blooms during the snowy winters of the southern Andes and whose flowers are visited by the hummingbird Sephanoides sephaniodes. The nectar produced by T. corymbosus represents the main food for overwintering populations of S. sephanioides, one of the principal pollinators in the temperate forest of southern South America. Hand-pollination experiments showed that this plant is fully self-compatible, with only a slight advantage of cross- over self-pollen during either germination or early tube growth. Despite self-compatibility, T. corymbosus exhibited a limited capacity for autonomous, within-flower pollination and high dependence on its hummingbird pollinator for full seed set. Thus, dwindling hummingbird populations should compromise reproductive success in this potential keystone plant species.
Long-term changes in vegetation, gradual and episodic, on the TGB Osborn Vegetation Reserve, Koonamore, South Australia (1926 - 2002)
Authors: Sinclair Russell
Published: June 2005

The TGB Osborn Vegetation Reserve at Koonamore, South Australia, is a 390-ha exclosure in semi-arid chenopod shrubland. The area was heavily overgrazed in 1925 when it was fenced to exclude sheep. Permanent quadrats and photopoints have been maintained to the present. Feral rabbits were sometimes numerous until the mid-1970s but have since been controlled. The records represent 50 years without sheep grazing, followed by 26 years without either sheep or rabbits. Dramatic seedling establishment events have occurred since 1978 for the following species: Acacia aneura Benth., Myoporum platycarpum R.Br., Senna artemesioides subsp. coriacea Randell, S. artemesioides subsp. petiolaris Randell, Acacia burkittii Benth., Dodonaea attenuata A.Cunn., Eremophila longifolia (R.Br.) F.Muell., E. sturtii R.Br. and Maireana pyramidata (Benth.) Paul G.Wilson. However, the chenopod shrubs Atriplex vesicaria Benth. and A. stipitata Benth. increased earlier and did not respond in the same way to episodic rainfall events or rabbit control. Numbers of Alectryon oleifolius (Desf.) S.T.Reynolds and Casuarina pauper F.Muell. ex L.A.S.Johnson have remained almost unchanged, whereas Maireana sedifolia (F.Muell.) Paul G.Wilson and M. astrotricha (L.Johnson) Paul G.Wilson have shown a very gradual increase over time. The data show evidence for both episodic and gradual change among different species.
Phytogeography and climate analysis of Nothofagus subgenus Brassospora in New Guinea and New Caledonia
Authors: Read Jennifer , Hope Geoffrey S. , Hill Robert S.
Published: June 2005

Nothofagus subgenus Brassospora now occurs only in New Guinea and New Caledonia, but is well known from fossil deposits of South America, New Zealand, Antarctica and Australia. It is commonly used for palaeoclimatic interpretation, but the climate characteristics of the extant species have not been described. In this paper we used the climatic estimation software, BIOCLIM, to derive a climate profile of 24 variables for each of the 14 species of Nothofagus native to New Guinea, and lapse rates and isohyet maps to describe the annual mean temperature and rainfall range of the five species native to New Caledonia. The New Guinea species occur at annual mean temperatures ranging from 10.6 to 23.5°C, with annual precipitation of 1762–7733 mm. The first three axes of a principal components analysis explained 85% of the total variation, the first axis comprising temperature variables, the second comprising precipitation range and precipitation of the wet season, and the third axis comprising dry-season precipitation and annual and diurnal temperature range. Some species had distinct combinations of positions along these component axes, indicating clear niche differentiation with respect to climate. The New Caledonian species occur at annual mean temperatures of 14.5–23.5°C, and annual precipitation of c. 1500–3500 mm. Although there was no significant difference in annual mean temperature and precipitation between the New Guinea and New Caledonian species, comparison of median values across species suggests specialisation of most New Caledonian species towards slightly drier conditions than the New Guinea species that occur at similarly high annual mean temperatures. Use of subgenus Brassospora to interpret palaeoclimates should take into account the variation in climate experienced across the range of extant species.
Evidence for simple genetic control of a fruit-colour polymorphism in Acacia ligulata
Authors: Whitney Kenneth D.
Published: June 2005

Fruit-colour polymorphisms are common in nature, but their genetic bases have rarely been examined in wild species. Here, I report on controlled crosses in Acacia ligulata A.Cunn. ex Benth., an Australian arid-zone shrub with a red–yellow–orange aril colour polymorphism. The evidence is consistent with 1-locus, 2-allele control of red v. yellow phenotypes; these phenotypes comprise 98.7% of the adult plants in nature. At this proposed r locus, yellow is dominant to red. Evidence concerning the rare orange morph is limited, but is consistent with models in which orange is produced by either (a) a third allele at the r locus or (b) modification by a second locus. Simple genetic architecture for ecologically relevant traits, such as fruit colour, should aid in linking ecological processes such as frugivory and seed dispersal to the evolutionary trajectories of plant populations.
Genetic diversity and mating system of an endangered tree Eucalyptus morrisbyi
Authors: Jones R. C. , McKinnon G. E. , Potts B. M. , Vaillancourt R. E.
Published: June 2005

Eucalyptus morrisbyi is an endangered eucalypt, restricted to four populations on the island of Tasmania. The two main populations are separated by 20 km, occurring in the Risdon Hills and on Calverts Hill, and differ markedly in size and health. Although they are both in reserves, the small population at Risdon Hills has experienced a marked decline in the last two decades. The other two populations (Lumeah Point and Honeywood Drive) are very small and under threat because of urbanisation. They are close to the large Calverts Hill population and may be remnants of a once larger population in this area prior to clearing for agriculture in the 19th century. A hypervariable chloroplast marker and six nuclear microsatellites, used to quantify genetic diversity among and within populations, indicated marked genetic differences between the two main populations (Risdon and Calverts Hills), with virtually no sharing of chloroplast haplotypes and little sharing of microsatellite alleles among populations. Both of the main populations are clearly required to adequately conserve the genetic diversity in this species, whereas the Lumeah Point and Honeywood Drive populations are similar to the proximal Calverts Hill population. The two main populations showed equally high levels of genetic diversity (average HE = 0.69) in the adult trees, using microsatellites, and little difference in inbreeding levels despite the large difference in population size. Analyses of 366 offspring from 9–11 trees from each main population revealed high outcrossing rates, little bi-parental inbreeding and high genetic diversity (average HE = 0.65) in both seedling populations. This indicates that open-pollinated seed collections from these populations capture sufficient genetic diversity for ex situ conservation plantings. It is argued that the high genetic diversity maintained in the small Risdon Hills population is due to a combination of the longevity of its genotypes (possibly up to 1155–1523 years) through a well developed mechanism of vegetative regeneration from lignotubers, coupled with high outcrossing rates maintained by a strong self-incompatibility mechanism.
Critical period for sensory experience-dependent survival of newly generated granule cells in the adult mouse olfactory bulb
Authors: Yamaguchi Masahiro , Mori Kensaku
Published: June 2005

Granule cells in the olfactory bulb (OB) are continually produced and added into the neuronal circuit in the adult brain. Sensory input to the OB plays a key role in the survival of newly generated granule cells. Here, we examined in the adult mice whether there is a time window after the generation of new granule cells when their survival is strongly influenced by sensory input. New granule cells were labeled by BrdUrd injection, and the mice were deprived of sensory input unilaterally by naris cauterization. During the initial 14 days after BrdUrd labeling, the number of BrdUrd-positive granule cells was similar for deprived and undeprived OBs. At 28 days or later, the BrdUrd-positive cell number remarkably decreased in the deprived OB. Cauterization at days 14–28 effectively reduced the number of BrdUrd-positive granule cells, whereas 2-week cauterization before or after this period produced little effect. Administration of diazepam, a GABA
A
receptor modulator, decreased the number of BrdUrd-positive granule cells. The diazepam administration was most effective at days 14–28. Histochemical examination showed that activation of caspase-3 was accompanied by apoptotic cell death of granule cells that was induced by sensory deprivation or diazepam administration. Double labeling with activated caspase-3 and BrdUrd indicated that granule cells at days 14–20 were most susceptible to cell death. These results indicate that there is a critical period when the survival of new granule cells is determined in a sensory experience-dependent manner and that the pharmacological manipulation can mimic the effect of sensory deprivation.
Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner
Authors: Li Yong , Choi Mihwa , Suino Kelly , Kovach Amanda , Daugherty Jennifer , Kliewer Steven A. , Xu H. Eric
Published: June 2005

The functional interaction between the orphan nuclear receptors small heterodimer partner (SHP) and liver receptor homolog 1 (LRH-1), where SHP binds to LRH-1 and represses its constitutive transcriptional activity, is crucial for regulating genes involved in cholesterol homeostasis. Here, we report structural and biochemical analyses of the LRH-1/SHP interaction. The crystal structure and modeling studies of the LRH-1 ligand-binding domain bound to either of the two LXXLL-related motifs of SHP show that the receptor undergoes conformational changes to accommodate the SHP docking and reveal key residues that determine the potency and selectivity of SHP binding. Through a combination of mutagenesis and binding studies, we demonstrate that only the second SHP LXXLL motif is required for repressing LRH-1, and this motif displays a strong preference for binding to LRH-1 over the closely related receptor steroidogeneic factor 1 (SF-1). Structural comparisons indicate that this binding selectivity is determined by residues flanking the core LXXLL motifs. These results establish a structural model for understanding how SHP interacts with LRH-1 to regulate cholesterol homeostasis and provide new insights into how nuclear receptor/coregulator selectivity is achieved.
Extreme hyperopia is the result of null mutations inMFRP, which encodes a Frizzled-related protein
Authors: Sundin Olof H. , Leppert Gregory S. , Silva Eduardo D. , Yang Jun-Ming , Dharmaraj Sharola , Maumenee Irene H. , Santos Luisa Coutinho , Parsa Cameron F. , Traboulsi Elias I. , Broman Karl W. , DiBernardo Cathy , Sunness Janet S. , Toy Jeffrey , Weinberg Ethan M.
Published: June 2005

Nanophthalmos is a rare disorder of eye development characterized by extreme hyperopia (farsightedness), with refractive error in the range of +8.00 to +25.00 diopters. Because the cornea and lens are normal in size and shape, hyperopia occurs because insufficient growth along the visual axis places these lensing components too close to the retina. Nanophthalmic eyes show considerable thickening of both the choroidal vascular bed and scleral coat, which provide nutritive and structural support for the retina. Thickening of these tissues is a general feature of axial hyperopia, whereas the opposite occurs in myopia. We have mapped recessive nanophthalmos to a unique locus at 11q23.3 and identified four independent mutations inMFRP, a gene that is selectively expressed in the eye and encodes a protein with homology to Tolloid proteases and the Wnt-binding domain of the Frizzled transmembrane receptors. This gene is not critical for retinal function, as patients entirely lackingMFRPcan still have good refraction-corrected vision, produce clinically normal electro-retinograms, and show only modest anomalies in the dark adaptation of photoreceptors.MFRPappears primarily devoted to regulating axial length of the eye. It remains to be determined whether natural variation in its activity plays a role in common refractive errors.
The impact of HIV/AIDS on the control of tuberculosis in India
Authors: Williams B. G. , Granich R. , Chauhan L. S. , Dharmshaktu N. S. , Dye C.
Published: June 2005

Epidemics of HIV/AIDS have increased the tuberculosis (TB) case-load by five or more times in East Africa and southern Africa. As HIV continues to spread, warnings have been issued of disastrous AIDS and TB epidemics in “new-wave” countries, including India, which accounts for 20% of all new TB cases arising in the world each year. Here we investigate whether, in the face of the HIV epidemic, India's Revised National TB Control Program (RNTCP) could halve TB prevalence and death rates in the period 1990–2015, as specified by the United Nations Millennium Development Goals. Using a mathematical model to capture the spatial and temporal variation in TB and HIV in India, we predict that, without the RNTCP, HIV would increase TB prevalence (by 1%), incidence (by 12%), and mortality rates (by 33%) between 1990 and 2015. With the RNTCP, however, we expect substantial reductions in prevalence (by 68%), incidence (by 41%), and mortality (by 39%) between 1990 and 2015. In India, 29% of adults but 72% of HIV-positive adults live in four large states in the south where, even with the RNTCP, mortality is expected to fall by only 15% between 1990 and 2015. Nationally, the RNTCP should be able to reverse the increases in TB burden due to HIV but, to ensure that TB mortality is reduced by 50% or more by 2015, HIV-infected TB patients should be provided with antiretroviral therapy in addition to the recommended treatment for TB.
IL-6 trans-signaling via STAT3 directs T cell infiltration in acute inflammation
Authors: McLoughlin Rachel M. , Jenkins Brendan J. , Grail Dianne , Williams Anwen S. , Fielding Ceri A. , Parker Clare R. , Ernst Matthias , Topley Nicholas , Jones Simon A.
Published: June 2005

Interleukin (IL)-6 signaling through its soluble receptor (IL-6 transsignaling) directs transition between innate and acquired immune responses by orchestrating the chemokine-directed attraction and apoptotic clearance of leukocytes. Through analysis of mononuclear cell infiltration in WT and IL-6-deficient mice during peritoneal inflammation, we now report that IL-6 selectively governs T cell infiltration by regulating chemokine secretion (CXCL10, CCL4, CCL5, CCL11, and CCL17) and chemokine receptor (CCR3, CCR4, CCR5, and CXCR3) expression on the CD3+infiltrate. Although blockade of IL-6 trans-signaling prevented chemokine release, chemokine receptor expression remained unaltered suggesting that this response is regulated by IL-6 itself. To dissect the signaling events promoting T cell migration, inflammation was established in knock-in mice expressing mutated forms of the universal signal-transducing element for IL-6-related cytokines gp130. In mice (gp130Y757F/Y757F) deficient in SHP2 and SOCS3 binding, but presenting hyperactivation of STAT1/3, T cell recruitment and CCL5 expression was enhanced. Conversely, both of these parameters were suppressed in mice with ablated gp130-mediated STAT1/3 activation (gp130ΔSTAT/ΔSTAT). T cell migration was related to STAT3 activity, because monoallelic deletion ofStat3ingp130Y757F/Y757Fmice (gp130Y757F/Y757F:Stat3+/-) corrected the exaggerated responses observed ingp130Y757F/Y757Fmice. Consequently, STAT3 plays a defining role in IL-6-mediated T cell migration.
Sparse nonnegative solution of underdetermined linear equations by linear programming
Authors: Donoho David L. , Tanner Jared
Published: June 2005

Consider an underdetermined system of linear equationsy=Axwith knownyandd×nmatrixA. We seek the nonnegativexwith the fewest nonzeros satisfyingy=Ax. In general, this problem is NP-hard. However, for many matricesAthere is a threshold phenomenon: if the sparsest solution is sufficiently sparse, it can be found by linear programming. We explain this by the theory of convex polytopes. Letajdenote thejth column ofA, 1 ≤j≤n, leta0= 0 andPdenote the convex hull of theaj. We say the polytopePis outwardlyk-neighborly if every subset ofkvertices not including 0 spans a face ofP. We show that outwardk-neighborliness is equivalent to the statement that, whenevery=Axhas a nonnegative solution with at mostknonzeros, it is the nonnegative solution toy=Axhaving minimal sum. We also consider weak neighborliness, where the overwhelming majority ofk-sets ofajs not containing 0 span a face ofP. This implies that most nonnegative vectorsxwithknonzeros are uniquely recoverable fromy=Axby linear programming. Numerous corollaries follow by invoking neighborliness results. For example, for most largenby 2nunderdetermined systems having a solution with fewer nonzeros than roughly half the number of equations, the sparsest solution can be found by linear programming.
The evolution of vertebrate Toll-like receptors
Authors: Roach Jared C. , Glusman Gustavo , Rowen Lee , Kaur Amardeep , Purcell Maureen K. , Smith Kelly D. , Hood Leroy E. , Aderem Alan
Published: June 2005

The complete sequences of
Takifugu
Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including
TLR1
has more species-specific adaptations than other families. A major family including
TLR11
is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12
Takifugu rubripes
TLRs. In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt.
On class differentials in educational attainment
Authors: Erikson Robert , Goldthorpe John H. , Jackson Michelle , Yaish Meir , Cox D. R.
Published: June 2005

Social class differentials in educational attainment have been extensively studied in numerous countries. In this paper, we begin by examining class differentials in the progression to higher secondary education among 16-year-old children in England and Wales. As has been shown for other countries, the differentials result both from the primary effects of differing levels of academic performance of children of different class background and from the secondary effects of differences in the educational choices that these children make at given levels of performance. Through counterfactual analyses in which the performance distribution of one class is combined with the choice distribution of another, primary and secondary effects are decomposed and the former are shown to be roughly three times the size of the latter.
The distribution of response spectra in the lateral geniculate nucleus compared with reflectance spectra of Munsell color chips
Authors: Romney A. Kimball , D'Andrade Roy G. , Indow Tarow
Published: June 2005

This paper compares the spectral response curves of cells in the lateral geniculate nucleus (LGN) with the reflectance spectra of a large sample of Munsell color chips. By examining the color chips with methods used by neural response researchers and the LGN cells with methods used by psychophysical color researchers, we obtain insights that may be useful for advancing knowledge in both fields. For LGN cells, the prevailing view is that they tend to be clustered into distinct types or along discernible lines or planes when data obtained from selected light stimuli are represented in a three-dimensional space derived from cone contributions. In contrast, the Munsell color chips are viewed as rather evenly distributed in a three-dimensional perceptual space based on the psychophysical judgment of surface colors. We demonstrate that, when the Munsell chips are viewed in the space typically applied to LGN cells, the distribution appears similar to that of the cells and vice versa. We show why this result occurs and suggest that it has implications for studies in both fields.
Reduced water density at hydrophobic surfaces: Effect of dissolved gases
Authors: Doshi Dhaval A. , Watkins Erik B. , Israelachvili Jacob N. , Majewski Jaroslaw
Published: June 2005

Here, direct noninvasive neutron reflectivity measurements reveal the presence of a reduced (deuterated) water density region, with a sigmoidal density profile at the hydrophobic silane–water interface that depends on the type and concentration of dissolved gases in the water. Removal of dissolved gases decreases the width of the reduced water density region, and their reintroduction leads to its increase. When compared with recent computer simulations, a locally fluctuating density profile is proposed, whereas preexisting nanobubbles are excluded. The presence of a fluctuating reduced water density region between two hydrophobic surfaces and the attractive “depletion force” to which it leads may help explain the hydrophobic force and its reported diminution in deaerated water. Our results are also quantitatively consistent with recent dynamic surface force apparatus results that drastically revise previous estimates of the slip length of water flowing past hydrophobic surfaces from microns to ≈20 nm. Our observations, therefore, go a long way toward reconciling three quite different types of experiments and phenomena: water depletion at hydrophobic surfaces, water slip at hydrophobic surfaces, and the hydrophobic interaction.
Coevolutionary arms races between bacteria and bacteriophage
Authors: Weitz J. S. , Hartman H. , Levin S. A.
Published: June 2005

We propose a computational and theoretical framework for analyzing rapid coevolutionary dynamics of bacteriophage and bacteria in their ecological context. Bacteriophage enter host cells via membrane-bound surface receptors often responsible for nutrient uptake. As such, a selective pressure will exist for the bacteria to modify its receptor configuration and, in turn, for the phage to modify its tail fiber. A mathematical model of these trait adaptations is developed by using the framework of adaptive dynamics. Host strains differ in their efficiency of resource uptake and resistance to phage, whereas phage strains differ in their host preference for adsorption. We solve the evolutionary ecology model and find the conditions for coevolutionary branching and relevant dimensionless parameters leading to distinct quasispecies. We confirm these calculations using stochastic Monte Carlo simulations of populations evolving in a chemostat with fixed washout rate and inflow resource density. We find that multiple quasispecies of bacteria and phage can coexist in a homogeneous medium with a single resource. When diversification occurs, quasispecies of phage adsorb effectively to only a limited subset of the total number of quasispecies of bacteria, i.e., functional differences between quasispecies arise endogenously within the evolutionary ecology framework. Finally, we discuss means to relate predictions of this model to experimental studies in the chemostat, using the model organismsEscherichia coliand the virulent strain of λ phage.
The human brain is intrinsically organized into dynamic, anticorrelated functional networks
Authors: Fox Michael D. , Snyder Abraham Z. , Vincent Justin L. , Corbetta Maurizio , Van Essen David C. , Raichle Marcus E.
Published: June 2005

During performance of attention-demanding cognitive tasks, certain regions of the brain routinely increase activity, whereas others routinely decrease activity. In this study, we investigate the extent to which this task-related dichotomy is represented intrinsically in the resting human brain through examination of spontaneous fluctuations in the functional MRI blood oxygen level-dependent signal. We identify two diametrically opposed, widely distributed brain networks on the basis of both spontaneous correlations within each network and anticorrelations between networks. One network consists of regions routinely exhibiting task-related activations and the other of regions routinely exhibiting task-related deactivations. This intrinsic organization, featuring the presence of anticorrelated networks in the absence of overt task performance, provides a critical context in which to understand brain function. We suggest that both task-driven neuronal responses and behavior are reflections of this dynamic, ongoing, functional organization of the brain.
The Rho GTP exchange factor Lfc promotes spindle assembly in early mitosis
Authors: Bakal Christopher J. , Finan Dina , LaRose José , Wells Clark D. , Gish Gerald , Kulkarni Sarang , DeSepulveda Paulo , Wilde Andrew , Rottapel Robert
Published: June 2005

Rho GTPases regulate reorganization of actin and microtubule cytoskeletal structures during both interphase and mitosis. The timing and subcellular compartment in which Rho GTPases are activated is controlled by the large family of Rho GTP exchange factors (RhoGEFs). Here, we show that the microtubule-associated RhoGEF Lfc is required for the formation of the mitotic spindle during prophase/prometaphase. The inability of cells to assemble a functioning spindle after Lfc inhibition resulted in a delay in mitosis and an accumulation of prometaphase cells. Inhibition of Lfc's primary target Rho GTPase during prophase/prometaphase, or expression of a catalytically inactive mutant of Lfc, also prevented normal spindle assembly and resulted in delays in mitotic progression. Coinjection of constitutively active Rho GTPase rescued the spindle defects caused by Lfc inhibition, suggesting the requirement of RhoGTP in regulating spindle assembly. Lastly, we implicate mDia1 as an important effector of Lfc signaling. These findings demonstrate a role for Lfc, Rho, and mDia1 during mitosis.
dGRASP Localization and Function in the Early Exocytic Pathway inDrosophilaS2 Cells
Authors: Kondylis Vangelis , Spoorendonk Kirsten M. , Rabouille Catherine
Published: June 2005

The de novo model for Golgi stack biogenesis predicts that membrane exiting the ER at transitional ER (tER) sites contains and recruits all the necessary molecules to form a Golgi stack, including the Golgi matrix proteins, p115, GM130, and GRASP65/55. These proteins leave the tER sites faster than Golgi transmembrane resident enzymes, suggesting that they act as a template nucleating the formation of the Golgi apparatus. However, the localization of the Golgi matrix proteins at tER sites is only shown under conditions where exit from the ER is blocked. Here, we show in Drosophila S2 cells, that dGRASP, the single Drosophila homologue of GRASP65/55, localizes both to the Golgi membranes and the tER sites at steady state and that the myristoylation of glycine 2 is essential for the localization to both compartments. Its depletion for 96 h by RNAi gave an effect on the architecture of the Golgi stacks in 30% of the cells, but a double depletion of dGRASP and dGM130 led to the quantitative conversion of Golgi stacks into clusters of vesicles and tubules, often featuring single cisternae. This disruption of Golgi architecture was not accompanied by the disorganization of tER sites or the inhibition of anterograde transport. This shows that, at least in Drosophila, the structural integrity of the Golgi stacks is not required for efficient transport. Overall, dGRASP exhibits a dynamic association to the membrane of the early exocytic pathway and is involved in Golgi stack architecture.
The Novel Fission Yeast Protein Pal1p Interacts with Hip1-related Sla2p/End4p and Is Involved in Cellular Morphogenesis
Authors: Ge Wanzhong , Chew Ting Gang , Wachtler Volker , Naqvi Suniti N. , Balasubramanian Mohan K.
Published: June 2005

The establishment and maintenance of characteristic cellular morphologies is a fundamental property of all cells. Here we describe Schizosaccharomyces pombe Pal1p, a protein important for maintenance of cylindrical cellular morphology. Pal1p is a novel membrane-associated protein that localizes to the growing tips of interphase cells and to the division site in cells undergoing cytokinesis in an F-actin- and microtubule-independent manner. Cells deleted for pal1 display morphological defects, characterized by the occurrence of spherical and pear-shaped cells with an abnormal cell wall. Pal1p physically interacts and displays overlapping localization with the Huntingtin-interacting-protein (Hip1)-related protein Sla2p/End4p, which is also required for establishment of cylindrical cellular morphology. Sla2p is important for efficient localization of Pal1p to the sites of polarized growth and appears to function upstream of Pal1p. Interestingly, spherical pal1Δ mutants polarize to establish a pearlike morphology before mitosis in a manner dependent on the kelch-repeat protein Tea1p and the cell cycle inhibitory kinase Wee1p. Thus, overlapping mechanisms involving Pal1p, Tea1p, and Sla2p contribute to the establishment of cylindrical cellular morphology, which is important for proper spatial regulation of cytokinesis.
GLUT1CBP(TIP2/GIPC1) Interactions with GLUT1 and Myosin VI: Evidence Supporting an Adapter Function for GLUT1CBP
Authors: Reed Brent C. , Cefalu Christopher , Bellaire Bryan H. , Cardelli James A. , Louis Thomas , Salamon Joanna , Bloecher Mari Anne , Bunn Robert C.
Published: June 2005

We identified a novel interaction between myosin VI and the GLUT1 transporter binding protein GLUT1CBP(GIPC1) and first proposed that as an adapter molecule it might function to couple vesicle-bound proteins to myosin VI movement. This study refines the model by identifying two myosin VI binding domains in the GIPC1 C terminus, assigning respective oligomerization and myosin VI binding functions to separate N- and C-terminal domains, and defining a central region in the myosin VI tail that binds GIPC1. Data further supporting the model demonstrate that 1) myosin VI and GIPC1 interactions do not require a mediating protein; 2) the myosin VI binding domain in GIPC1 is necessary for intracellular interactions of GIPC1 with myosin VI and recruitment of overexpressed myosin VI to membrane structures, but not for the association of GIPC1 with such structures; 3) GIPC1/myosin VI complexes coordinately move within cellular extensions of the cell in an actin-dependent and microtubule-independent manner; and 4) blocking either GIPC1 interactions with myosin VI or GLUT1 interactions with GIPC1 disrupts normal GLUT1 trafficking in polarized epithelial cells, leading to a reduction in the level of GLUT1 in the plasma membrane and concomitant accumulation in internal membrane structures.
Inhibition ofPkhd1Impairs Tubulomorphogenesis of Cultured IMCD Cells
Authors: Mai Weiyi , Chen Dong , Ding Tianbing , Kim Ingyu , Park Sujun , Cho Sae-youll , Chu Julia S.F. , Liang Dan , Wang Ning , Wu Dianqing , Li Song , Zhao Ping , Zent Roy , Wu Guanqing
Published: June 2005

Fibrocystin/polyductin (FPC), the gene product of PKHD1, is responsible for autosomal recessive polycystic kidney disease (ARPKD). This disease is characterized by symmetrically large kidneys with ectasia of collecting ducts. In the kidney, FPC predominantly localizes to the apical domain of tubule cells, where it associates with the basal bodies/primary cilia; however, the functional role of this protein is still unknown. In this study, we established stable IMCD (mouse inner medullary collecting duct) cell lines, in which FPC was silenced by short hairpin RNA inhibition (shRNA). We showed that inhibition of FPC disrupted tubulomorphogenesis of IMCD cells grown in three-dimensional cultures. Pkhd1-silenced cells developed abnormalities in cell-cell contact, actin cytoskeleton organization, cell-ECM interactions, cell proliferation, and apoptosis, which may be mediated by dysregulation of extracellular-regulated kinase (ERK) and focal adhesion kinase (FAK) signaling. These alterations in cell function in vitro may explain the characteristics of ARPKD phenotypes in vivo.
Yeast Aconitase in Two Locations and Two Metabolic Pathways: Seeing Small Amounts Is Believing
Authors: Regev-Rudzki Neta , Karniely Sharon , Ben-Haim Nitzan Natani , Pines Ophry
Published: June 2005

The distribution of identical enzymatic activities between different subcellular compartments is a fundamental process of living cells. At present, the Saccharomyces cerevisiae aconitase enzyme has been detected only in mitochondria, where it functions in the tricarboxylic acid (TCA) cycle and is considered a mitochondrial matrix marker. We developed two strategies for physical and functional detection of aconitase in the yeast cytosol: 1) we fused the α peptide of the β-galactosidase enzyme to aconitase and observed α complementation in the cytosol; and 2) we created an ACO1-URA3 hybrid gene, which allowed isolation of strains in which the hybrid protein is exclusively targeted to mitochondria. These strains display a specific phenotype consistent with glyoxylate shunt elimination. Together, our data indicate that yeast aconitase isoenzymes distribute between two distinct subcellular compartments and participate in two separate metabolic pathways; the glyoxylate shunt in the cytosol and the TCA cycle in mitochondria. We maintain that such dual distribution phenomena have a wider occurrence than recorded currently, the reason being that in certain cases there is a small fraction of one of the isoenzymes, in one of the locations, making its detection very difficult. We term this phenomenon of highly uneven isoenzyme distribution “eclipsed distribution.”
DrosophilaMob Family Proteins Interact with the Related Tricornered (Trc) and Warts (Wts) Kinases
Authors: He Ying , Emoto Kazuo , Fang Xiaolan , Ren Nan , Tian Xiaojing , Jan Yuh-Nung , Adler Paul N.
Published: June 2005

The function of Tricornered (Trc), the Drosophila Ndr (Nuclear Dbf2-related) serine/threonine protein kinase, is required for the normal morphogenesis of a variety of polarized outgrowths including epidermal hairs, bristles, arista laterals, and dendrites. In yeast the Trc homolog Cbk1 needs to bind Mob2 to activate the RAM pathway. In this report, we provide genetic and biochemical data that Drosophila Trc also interacts with and is activated by Drosophila Dmob proteins. In addition, Drosophila Mob proteins appear to interact with the related Warts/Lats kinase, which functions as a tumor suppressor in flies and mammals. Interestingly, the overgrowth tumor phenotype that results from mutations in Dmob1 (mats) was only seen in genetic mosaics and not when the entire animal was mutant. We conclude that unlike in yeast, in Drosophila individual Mob proteins interact with multiple kinases and that individual NDR family kinases interact with multiple Mob proteins. We further provide evidence that Mo25, the Drosophila homolog of the RAM pathway hym1 gene does not function along with Trc.
Role for Gcs1p in Regulation of Arl1p atTrans-Golgi Compartments
Authors: Liu Ya-Wen , Huang Chun-Fang , Huang Kai-Bin , Lee Fang-Jen S.
Published: June 2005

ADP-ribosylation factor (ARF) and ARF-like (ARL) proteins are members of the ARF family, which are critical components of several different vesicular trafficking pathways. ARFs have little or no detectable GTPase activity without the assistance of a GTPase-activating protein (GAP). Here, we demonstrate that yeast Gcs1p exhibits GAP activity toward Arl1p and Arf1p in vitro, and Arl1p can interact with Gcs1p in a GTP-dependent manner. Arl1p was observed both on trans-Golgi and in cytosol and was recruited from cytosol to membranes in a GTP-dependent manner. In gcs1 mutant cells, the fraction of Arl1p in cytosol relative to trans-Golgi was less than it was in wild-type cells. Increasing Gcs1p levels returned the distribution toward that of wild-type cells. Both Arl1p and Gcs1p influenced the distribution of Imh1p, an Arl1p effector. Our data are consistent with the conclusion that Arl1p moves in a dynamic equilibrium between trans-Golgi and cytosol, and the release of Arl1p from membranes in cells requires the hydrolysis of bound GTP, which is accelerated by Gcs1p.
APlasmodiumActin-depolymerizing Factor That Binds Exclusively to Actin Monomers
Authors: Schüler Herwig , Mueller Ann-Kristin , Matuschewski Kai
Published: June 2005

ADF/cofilins (AC) are essential F- and G-actin binding proteins that modulate microfilament turnover. The genome of Plasmodium falciparum, the parasite causing malaria, contains two members of the AC family. Interestingly, P. falciparum ADF1 lacks the F-actin binding residues of the AC consensus. Reverse genetics in the rodent malaria model system suggest that ADF1 performs vital functions during the pathogenic red blood cell stages, whereas ADF2 is not present in these stages. We show that recombinant PfADF1 interacts with monomeric actin but does not bind to actin polymers. Although other AC proteins inhibit nucleotide exchange on monomeric actin, the Plasmodium ortholog stimulates nucleotide exchange. Thus, PfADF1 differs in its biochemical properties from previously known AC proteins and seems to promote turnover exclusively by interaction with actin monomers. These findings provide important insights into the low cytosolic abundance and unique turnover characteristics of actin polymers in parasites of the phylum Apicomplexa.
A Novel Role for Integrin-linked Kinase in Epithelial Sheet Morphogenesis
Authors: Vespa Alisa , D'Souza Sudhir J.A. , Dagnino Lina
Published: June 2005

Integrin-linked kinase (ILK) is a multidomain protein involved in cell motility and cell-extracellular matrix interactions. ILK is found in integrin-containing focal adhesions in undifferentiated primary epidermal keratinocytes. Induction of keratinocyte differentiation by treatment with Ca2+triggers formation of cell–cell junctions, loss of focal adhesions, and ILK distribution to cell borders. We now show that Ca2+treatment of keratinocytes induces rapid (≤1 h) translocation to the cell membrane of the adherens junction (AJ) proteins E-cadherin and β-catenin. This is followed by slower (>6 h) localization of tight junction (TJ) proteins. The kinetics of ILK movement toward the cell periphery mimics that of AJ components, suggesting that ILK plays a role in the early formation of cell–cell contacts. Whereas the N terminus in ILK mediates localization to cell borders, expression of an ILK deletion mutant incapable of localizing to the cell membrane (ILK 191-452) interferes with translocation of E-cadherin/β-catenin to cell borders, precluding Ca2+-induced AJ formation. Cells expressing ILK 191-452 also fail to form TJ and sealed cell–cell borders and do not form epithelial sheets. Thus, we have uncovered a novel role for ILK in epithelial cell–cell adhesion, independent of its well-established role in integrin-mediated adhesion and migration.