bluuebunny/crossref_metadata_2025 huggingface dataset:
Accretion of the Earth
Authors: Canup Robin M
Published: October 2008

The origin of the Earth and its Moon has been the focus of an enormous body of research. In this paper I review some of the current models of terrestrial planet accretion, and discuss assumptions common to most works that may require re-examination. Density-wave interactions between growing planets and the gas nebula may help to explain the current near-circular orbits of the Earth and Venus, and may result in large-scale radial migration of proto-planetary embryos. Migration would weaken the link between the present locations of the planets and the original provenance of the material that formed them. Fragmentation can potentially lead to faster accretion and could also damp final planet orbital eccentricities. The Moon-forming impact is believed to be the final major event in the Earth's accretion. Successful simulations of lunar-forming impacts involve a differentiated impactor containing between 0.1 and 0.2 Earth masses, an impact angle near 45° and an impact speed within 10 per cent of the Earth's escape velocity. All successful impacts—with or without pre-impact rotation—imply that the Moon formed primarily from material originating from the impactor rather than from the proto-Earth. This must ultimately be reconciled with compositional similarities between the Earth and the Moon.
Collisional erosion and the non-chondritic composition of the terrestrial planets
Authors: O'Neill Hugh St.C , Palme Herbert
Published: October 2008

The compositional variations among the chondrites inform us about cosmochemical fractionation processes during condensation and aggregation of solid matter from the solar nebula. These fractionations include: (i) variable Mg–Si–RLE ratios (RLE: refractory lithophile element), (ii) depletions in elements more volatile than Mg, (iii) a cosmochemical metal–silicate fractionation, and (iv) variations in oxidation state. Moon- to Mars-sized planetary bodies, formed by rapid accretion of chondrite-like planetesimals in local feeding zones within 106years, may exhibit some of these chemical variations. However, the next stage of planetary accretion is the growth of the terrestrial planets from approximately 102embryos sourced across wide heliocentric distances, involving energetic collisions, in which material may be lost from a growing planet as well as gained. While this may result in averaging out of the ‘chondritic’ fractionations, it introduces two non-chondritic chemical fractionation processes: post-nebular volatilization and preferential collisional erosion. In the latter, geochemically enriched crust formed previously is preferentially lost. That post-nebular volatilization was widespread is demonstrated by the non-chondritic Mn/Na ratio in all the small, differentiated, rocky bodies for which we have basaltic samples, including the Moon and Mars. The bulk silicate Earth (BSE) has chondritic Mn/Na, but shows several other compositional features in its pattern of depletion of volatile elements suggestive of non-chondritic fractionation. The whole-Earth Fe/Mg ratio is 2.1±0.1, significantly greater than the solar ratio of 1.9±0.1, implying net collisional erosion of approximately 10 per cent silicate relative to metal during the Earth's accretion. If this collisional erosion preferentially removed differentiated crust, the assumption of chondritic ratios among all RLEs in the BSE would not be valid, with the BSE depleted in elements according to their geochemical incompatibility. In the extreme case, the Earth would only have half the chondritic abundances of the highly incompatible, heat-producing elements Th, U and K. Such an Earth model resolves several geochemical paradoxes: the depleted mantle occupies the whole mantle, is completely outgassed in40Ar and produces the observed4He flux through the ocean basins. But the lower radiogenic heat production exacerbates the discrepancy with heat loss.
What CO
2
well gases tell us about the origin of noble gases in the mantle and their relationship to the atmosphere
Authors: Ballentine Chris J , Holland Greg
Published: October 2008

Study of commercially produced volcanic CO
2
gas associated with the Colorado Plateau, USA, has revealed substantial new information about the noble gas isotopic composition and elemental abundance pattern of the mantle. Combined with published data from mid-ocean ridge basalts, it is now clear that the convecting mantle has a maximum
20
Ne/
22
Ne isotopic composition, indistinguishable from that attributed to solar wind-implanted (SWI) neon in meteorites. This is distinct from the higher
20
Ne/
22
Ne isotopic value expected for solar nebula gases. The non-radiogenic xenon isotopic composition of the well gases shows that 20 per cent of the mantle Xe is ‘solar-like’ in origin, but cannot resolve the small isotopic difference between the trapped meteorite ‘Q’-component and solar Xe. The mantle primordial
20
Ne/
132
Xe is approximately 1400 and is comparable with the upper end of that observed in meteorites. Previous work using the terrestrial
129
I–
129
Xe mass balance demands that almost 99 per cent of the Xe (and therefore other noble gases) has been lost from the accreting solids and that Pu–I closure age models have shown this to have occurred in the first
ca
100 Ma of the Earth's history. The highest concentrations of Q-Xe and solar wind-implanted (SWI)-Ne measured in meteorites allow for this loss and these high-abundance samples have a Ne/Xe ratio range compatible with the ‘recycled-air-corrected’ terrestrial mantle. These observations do not support models in which the terrestrial mantle acquired its volatiles from the primary capture of solar nebula gases and, in turn, strongly suggest that the primary terrestrial atmosphere, before isotopic fractionation, is most probably derived from degassed trapped volatiles in accreting material.

By contrast, the non-radiogenic argon, krypton and 80 per cent of the xenon in the convecting mantle have the same isotopic composition and elemental abundance pattern as that found in seawater with a small sedimentary Kr and Xe admix. These mantle heavy noble gases are dominated by recycling of air dissolved in seawater back into the mantle. Numerical simulations suggest that plumes sampling the core–mantle boundary would be enriched in seawater-derived noble gases compared with the convecting mantle, and therefore have substantially lower
40
Ar/
36
Ar. This is compatible with observation. The subduction process is not a complete barrier to volatile return to the mantle.
Composition of the Earth's interior: the importance of early events
Authors: Carlson Richard W , Boyet Maud
Published: October 2008

The detection of excess142Nd caused by the decay of 103 Ma half-life146Sm in all terrestrial rocks compared with chondrites shows that the chondrite analogue compositional model cannot be strictly correct, at least for the accessible portion of the Earth. Both the continental crust (CC) and the mantle source of mid-ocean ridge basalts (MORB) originate from the material characterized by superchondritic142Nd/144Nd. Thus, the mass balance of CC plus mantle depleted by crust extraction (the MORB-source mantle) does not sum back to chondritic compositions, but instead to a composition with Sm/Nd ratio sufficiently high to explain the superchondritic142Nd/144Nd. This requires that the mass of mantle depleted by CC extraction expand to 75–100 per cent of the mantle depending on the composition assumed for average CC. If the bulk silicate Earth has chondritic relative abundances of the refractory lithophile elements, then there must exist within the Earth's interior an incompatible-element-enriched reservoir that contains roughly 40 per cent of the Earth's40Ar and heat-producing radioactive elements. The existence of this enriched reservoir is demonstrated by time-varying142Nd/144Nd in Archaean crustal rocks. Calculations of the mass of the enriched reservoir along with seismically determined properties of the D″ layer at the base of the mantle allow the speculation that this enriched reservoir formed by the sinking of dense melts deep in a terrestrial magma ocean. The enriched reservoir may now be confined to the base of the mantle owing to a combination of compositionally induced high density and low viscosity, both of which allow only minimal entrainment into the overlying convecting mantle.
Isotopes as clues to the origin and earliest differentiation history of the Earth
Authors: Jacobsen Stein B , Ranen Michael C , Petaev Michael I , Remo John L , O'Connell Richard J , Sasselov Dimitar D
Published: October 2008

Measurable variations in182W/183W,142Nd/144Nd,129Xe/130Xe and136XePu/130Xe in the Earth and meteorites provide a record of accretion and formation of the core, early crust and atmosphere. These variations are due to the decay of the now extinct nuclides182Hf,146Sm,129I and244Pu. Thel82Hf–182W system is the best accretion and core-formation chronometer, which yields a mean time of Earth's formation of 10 Myr, and a total time scale of 30 Myr. New laser shock data at conditions comparable with those in the Earth's deep mantle subsequent to the giant Moon-forming impact suggest that metal–silicate equilibration was rapid enough for the Hf–W chronometer to reliably record this time scale. The coupled146Sm–147Sm chronometer is the best system for determining the initial silicate differentiation (magma ocean crystallization and proto-crust formation), which took place atca4.47 Ga or perhaps even earlier. The presence of a large129Xe excess in the deep Earth is consistent with a very early atmosphere formation (as early as 30 Myr); however, the interpretation is complicated by the fact that most of the atmospheric Xe may be from a volatile-rich late veneer.
New geochemical insights into volcanic degassing
Authors: Edmonds Marie
Published: October 2008

Magma degassing plays a fundamental role in controlling the style of volcanic eruptions. Whether a volcanic eruption is explosive, or effusive, is of crucial importance to approximately 500 million people living in the shadow of hazardous volcanoes worldwide. Studies of how gases exsolve and separate from magma prior to and during eruptions have been given new impetus by the emergence of more accurate and automated methods to measure volatile species both as volcanic gases and dissolved in the glasses of erupted products. The composition of volcanic gases is dependent on a number of factors, the most important being magma composition and the depth of gas–melt segregation prior to eruption; this latter parameter has proved difficult to constrain in the past, yet is arguably the most critical for controlling eruptive style. Spectroscopic techniques operating in the infrared have proved to be of great value in measuring the composition of gases at high temporal resolution. Such methods, when used in tandem with microanalytical geochemical investigations of erupted products, are leading to better constraints on the depth at which gases are generated and separated from magma. A number of recent studies have focused on transitions between explosive and effusive activity and have led to a better understanding of gas–melt segregation at basaltic volcanoes. Other studies have focused on degassing during intermediate and silicic eruptions. Important new results include the recognition of fluxing by deep-derived gases, which buffer the amount of dissolved volatiles in the melt at shallow depths, and the observation of gas flow up permeable conduit wall shear zones, which may be the primary mechanism for gas loss at the cusp of the most explosive and unpredictable volcanic eruptions. In this paper, I review current and future directions in the field of geochemical studies of volcanic degassing processes and illustrate how the new insights are beginning to change the way in which we understand and classify volcanic eruptions.
Experiments on metal–silicate plumes and core formation
Authors: Olson Peter , Weeraratne Dayanthie
Published: October 2008

Short-lived isotope systematics, mantle siderophile abundances and the power requirements of the geodynamo favour an early and high-temperature core-formation process, in which metals concentrate and partially equilibrate with silicates in a deep magma ocean before descending to the core. We report results of laboratory experiments on liquid metal dynamics in a two-layer stratified viscous fluid, using sucrose solutions to represent the magma ocean and the crystalline, more primitive mantle and liquid gallium to represent the core-forming metals. Single gallium drop experiments and experiments on Rayleigh–Taylor instabilities with gallium layers and gallium mixtures produce metal diapirs that entrain the less viscous upper layer fluid and produce trailing plume conduits in the high-viscosity lower layer. Calculations indicate that viscous dissipation in metal–silicate plumes in the early Earth would result in a large initial core superheat. Our experiments suggest that metal–silicate mantle plumes facilitate high-pressure metal–silicate interaction and may later evolve into buoyant thermal plumes, connecting core formation to ancient hotspot activity on the Earth and possibly on other terrestrial planets.
Boreal forests, aerosols and the impacts on clouds and climate
Authors: Spracklen Dominick V , Bonn Boris , Carslaw Kenneth S
Published: October 2008

Previous studies have concluded that boreal forests warm the climate because the cooling from storage of carbon in vegetation and soils is cancelled out by the warming due to the absorption of the Sun's heat by the dark forest canopy. However, these studies ignored the impacts of forests on atmospheric aerosol. We use a global atmospheric model to show that, through emission of organic vapours and the resulting condensational growth of newly formed particles, boreal forests double regional cloud condensation nuclei concentrations (from approx. 100 to approx. 200 cm
−3
). Using a simple radiative model, we estimate that the resulting change in cloud albedo causes a radiative forcing of between −1.8 and −6.7 W m
−2
of forest. This forcing may be sufficiently large to result in boreal forests having an overall cooling impact on climate. We propose that the combination of climate forcings related to boreal forests may result in an important global homeostasis. In cold climatic conditions, the snow–vegetation albedo effect dominates and boreal forests warm the climate, whereas in warmer climates they may emit sufficiently large amounts of organic vapour modifying cloud albedo and acting to cool climate.
A young Moon-forming giant impact at 70–110 million years accompanied by late-stage mixing, core formation and degassing of the Earth
Authors: Halliday Alex N
Published: October 2008

New W isotope data for lunar metals demonstrate that the Moon formed late in isotopic equilibrium with the bulk silicate Earth (BSE). On this basis, lunar Sr isotope data are used to define the former composition of the Earth and hence the Rb–Sr age of the Moon, which is 4.48±0.02 Ga, or 70–110 Ma (million years) after the start of the Solar System. This age is significantly later than had been deduced from W isotopes based on model assumptions or isotopic effects now known to be cosmogenic. The Sr age is in excellent agreement with earlier estimates based on the time of lunar Pb loss and the age of the early lunar crust (4.46±0.04 Ga). Similar ages for the BSE are recorded by xenon and lead–lead, providing evidence of catastrophic terrestrial degassing, atmospheric blow-off and significant late core formation accompanying theca100 Ma giant impact. Agreement between the age of the Moon based on the Earth's Rb/Sr and the lead–lead age of the Moon is consistent with no major losses of moderately volatile elements from the Earth during the giant impact. The W isotopic composition of the BSE can be explained by end member models of (i) gradual accretion with a mean life of roughly 35 Ma or (ii) rapid growth with a mean life of roughly 10 Ma, followed by a significant hiatus prior to the giant impact. The former assumes that approximately 60 per cent of the incoming metal from impactors is added directly to the core during accretion. The latter includes complete mixing of all the impactor material into the BSE during accretion. The identical W isotopic composition of the Moon and the BSE limits the amount of material that can be added as a late veneer to the Earth after the giant impact to less than 0.3±0.3 per cent of ordinary chondrite or less than 0.5±0.6 per cent CI carbonaceous chondrite based on their known W isotopic compositions. Neither of these on their own is sufficient to explain the inventories of both refractory siderophiles such as platinum group elements and rhenium, and volatiles such as sulphur, carbon and water.
HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1
Authors: Miotto Benoit , Struhl Kevin
Published: October 2008

HBO1 histone acetylase is important for DNA replication licensing. In human cells, HBO1 associates with replication origins specifically during the G1 phase of the cell cycle in a manner that depends on the replication licensing factor Cdt1, but is independent of the Cdt1 repressor Geminin. HBO1 directly interacts with Cdt1, and it enhances Cdt1-dependent rereplication. Thus, HBO1 plays a direct role at replication origins as a coactivator of the Cdt1 licensing factor. As HBO1 is also a transcriptional coactivator, it has the potential to integrate internal and external stimuli to coordinate transcriptional responses with initiation of DNA replication.
A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb
Authors: Vokes Steven A. , Ji Hongkai , Wong Wing H. , McMahon Andrew P.
Published: October 2008

Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We characterized the Gli-dependent cis-regulatory network through a combination of whole-genome chromatin immunoprecipitation (ChIP)-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified ∼5000 high-quality Gli3-binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes. A subset of putative cis-regulatory regions were analyzed in transgenic embryos, establishing Blimp1 as a direct Gli target and identifying Gli activator signaling in a direct, long-range regulation of the BMP antagonist Gremlin. In contrast, a long-range silencer cassette downstream from Hand2 likely mediates Gli3 repression in the anterior limb. These studies provide the first comprehensive characterization of the transcriptional output of a Shh-patterning process in the mammalian embryo and a framework for elaborating regulatory networks in the developing limb.
The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression
Authors: Shema Efrat , Tirosh Itay , Aylon Yael , Huang Jing , Ye Chaoyang , Moskovits Neta , Raver-Shapira Nina , Minsky Neri , Pirngruber Judith , Tarcic Gabi , Hublarova Pavla , Moyal Lilach , Gana-Weisz Mali , Shiloh Yosef , Yarden Yossef , Johnsen Steven A. , Vojtesek Borivoj , Berger Shelley L. , Oren Moshe
Published: October 2008

Histone monoubiquitylation is implicated in critical regulatory processes. We explored the roles of histone H2B ubiquitylation in human cells by reducing the expression of hBRE1/RNF20, the major H2B-specific E3 ubiquitin ligase. While H2B ubiquitylation is broadly associated with transcribed genes, only a subset of genes was transcriptionally affected by RNF20 depletion and abrogation of H2B ubiquitylation. Gene expression dependent on RNF20 includes histones H2A and H2B and the p53 tumor suppressor. In contrast, RNF20 suppresses the expression of several proto-oncogenes, which reside preferentially in closed chromatin and are modestly transcribed despite bearing marks usually associated with high transcription rates. Remarkably, RNF20 depletion augmented the transcriptional effects of epidermal growth factor (EGF), increased cell migration, and elicited transformation and tumorigenesis. Furthermore, frequentRNF20promoter hypermethylation was observed in tumors. RNF20 may thus be a putative tumor suppressor, acting through selective regulation of a distinct subset of genes.
Polo-like kinase Cdc5 drives exit from pachytene during budding yeast meiosis
Authors: Sourirajan Anuradha , Lichten Michael
Published: October 2008

In budding yeast, exit from the pachytene stage of meiosis requires the mid-meiosis transcription factor Ndt80, which promotes expression of ∼200 genes. Ndt80 is required for meiotic function of polo-like kinase (PLK, Cdc5) and cyclin-dependent kinase (CDK), two cell cycle kinases previously implicated in pachytene exit. We show that ongoing CDK activity is dispensable for two events that accompany exit from pachytene: crossover formation and synaptonemal complex breakdown. In contrast, CDC5 expression in ndt80Δ mutants efficiently promotes both events. Thus, Cdc5 is the only member of the Ndt80 transcriptome required for this critical step in meiotic progression.
The jury is in: p73 is a tumor suppressor after all: Figure 1.
Authors: Rosenbluth Jennifer M. , Pietenpol Jennifer A.
Published: October 2008

While p53 has been extensively characterized as a tumor suppressor, it has been more difficult to determine whether p63 and/or p73 play a similar role. Every system in which these family members have been studied, from cells to animal models to human tissues, seems to create more questions than answers. Tomasini and colleagues (2677-2691) demonstrate that one isoform of p73 is responsible for preventing tumor formation in vivo, providing critical validation of an isoform-based model of p73 function.
SHC-1/p52Shc targets the insulin/IGF-1 and JNK signaling pathways to modulate life span and stress response in C. elegans
Authors: Neumann-Haefelin Elke , Qi Wenjing , Finkbeiner Elisabeth , Walz Gerd , Baumeister Ralf , Hertweck Maren
Published: October 2008

Correlative evidence links stress, accumulation of oxidative cellular damage, and aging in several species. Genetic studies in species ranging from yeast to mammals revealed several pathways regulating stress response and life span, including caloric intake, mitochondrial respiration, insulin/IGF-1 (IIS), and JNK (c-Jun N-terminal kinase) signaling. How IIS and JNK signaling cross-talk to defend against diverse stressors contributing to aging is of critical importance but, so far, only poorly understood. In this study, we demonstrate that the adaptor protein SHC-1, the Caenorhabditis elegans homolog of human p52Shc, coordinates mechanisms of stress response and aging. Using genetic and biochemical approaches, we discover that SHC-1 not only opposes IIS but also activates JNK signaling. Loss of shc-1 function results in accelerated aging and enhanced sensitivity to heat, oxidative stress, and heavy metals, whereas expression of human p52Shc rescues the shc-1 mutant phenotype. SHC-1 acts upstream of the insulin/IGF receptor DAF-2 and the PI3 kinase AGE-1 and directly interacts with DAF-2. Moreover, SHC-1 activates JNK signaling by binding to MEK-1 kinase. Both aspects converge on controlling the nuclear translocation and activation of the FOXO transcription factor DAF-16. Our findings establish C. elegans SHC-1 as a critical scaffold that directly cross-connects the two parallel JNK and IIS pathways and help to explain how these signaling cascades cooperate to ascertain normal stress response and life span in C. elegans.
Histone deacetylase 3 is required for centromeric H3K4 deacetylation and sister chromatid cohesion
Authors: Eot-Houllier Grégory , Fulcrand Géraldine , Watanabe Yoshinori , Magnaghi-Jaulin Laura , Jaulin Christian
Published: October 2008

We describe here the role of histone deacetylase 3 (HDAC3) in sister chromatid cohesion and the deacetylation of histone H3 Lys 4 (H3K4) at the centromere. HDAC3 knockdown induced spindle assembly checkpoint activation and sister chromatid dissociation. The depletion of Polo-like kinase 1 (Plk1) or Aurora B restored cohesion in HDAC3-depleted cells. HDAC3 was also required for Shugoshin localization at centromeres. Finally, we show that HDAC3 depletion results in the acetylation of centromeric H3K4, correlated with a loss of dimethylation at the same position. These findings provide a functional link between sister chromatid cohesion and the mitotic “histone code”.
Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo
Authors: Jedrusik Agnieszka , Parfitt David-Emlyn , Guo Guoji , Skamagki Maria , Grabarek Joanna B. , Johnson Martin H. , Robson Paul , Zernicka-Goetz Magdalena
Published: October 2008

Genesis of the trophectoderm and inner cell mass (ICM) lineages occurs in two stages. It is initiated via asymmetric divisions of eight- and 16-cell blastomeres that allocate cells to inner and outer positions, each with different developmental fates. Outside cells become committed to the trophectoderm at the blastocyst stage through Cdx2 activity, but here we show that Cdx2 can also act earlier to influence cell allocation. Increasing Cdx2 levels in individual blastomeres promotes symmetric divisions, thereby allocating more cells to the trophectoderm, whereas reducing Cdx2 promotes asymmetric divisions and consequently contribution to the ICM. Furthermore, both Cdx2 mRNA and protein levels are heterogeneous at the eight-cell stage. This heterogeneity depends on cell origin and has developmental consequences. Cdx2 expression is minimal in cells with unrestricted developmental potential that contribute preferentially to the ICM and is maximal in cells with reduced potential that contribute more to the trophectoderm. Finally, we describe a mutually reinforcing relationship between cellular polarity and Cdx2: Cdx2 influences cell polarity by up-regulating aPKC, but cell polarity also influences Cdx2 through asymmetric distribution of Cdx2 mRNA in polarized blastomeres. Thus, divisions generating inside and outside cells are truly asymmetric with respect to cell fate instructions. These two interacting effects ensure the generation of a stable outer epithelium by the blastocyst stage.
The Genus Antirrhinum (Snapdragon): A Flowering Plant Model for Evolution and Development
Authors: Hudson Andrew , Critchley Joanna , Erasmus Yvette
Published: October 2008

INTRODUCTION

The Antirrhinum species group comprises approximately 20 morphologically diverse members that are able to form fertile hybrids. It includes the cultivated snapdragon Antirrhinum majus, which has been used as a model for biochemical and developmental genetics for more than 75 yr. The research infrastructure for A. majus, together with the interfertility of the species group, allows Antirrhinum to be used to examine the genetic basis for plant diversity.
Planarians: A Versatile and Powerful Model System for Molecular Studies of Regeneration, Adult Stem Cell Regulation, Aging, and Behavior
Authors: Oviedo Néstor J. , Nicolas Cindy L. , Adams Dany S. , Levin Michael
Published: October 2008

INTRODUCTION

In recent years, planarians have been increasingly recognized as an emerging model organism amenable to molecular genetic techniques aimed at understanding complex biological tasks commonly observed among metazoans. Growing evidence suggests that this model organism is uniquely poised to inform us about the mechanisms of tissue regeneration, stem cell regulation, tissue turnover, pharmacological action of diverse drugs, cancer, and aging. This article provides an overview of the planarian model system with special attention to the species Schmidtea mediterranea. Additionally, information is provided about the most popular use of this organism, together with modern genomic resources and technical approaches.
Cultivating Antirrhinum
Authors: Hudson Andrew , Critchley Joanna , Erasmus Yvette
Published: October 2008

INTRODUCTION

In this protocol, we describe methods for cultivating Antirrhinum (snapdragon) species. These plants are easily grown, provided that they have sufficient light and are not overwatered. In good conditions, most species will flower and produce seeds within 3-4 mo. Strongly growing plants should suffer from few pests or diseases, but we also prescribe methods for dealing with microbes and insects that commonly damage Antirrhinum.
Isolation of Pristionchus Nematodes from Beetles
Authors: Rae Robbie , Schlager Benjamin , Sommer Ralf J.
Published: October 2008

INTRODUCTION

In this procedure, nematodes disembark from a beetle carcass and feed on Escherichia coli OP50. The nematodes are then monitored for a few days and identified using simple morphological characteristics. This method is rapid, easy, and biased for Pristionchus species.
Detection of Cell Proliferation in Spider Embryos Using BrdU Labeling
Authors: Prpic Nikola-Michael , Schoppmeier Michael , Damen Wim G.M.
Published: October 2008

INTRODUCTION

The spider Cupiennius salei, commonly known as the American wandering spider, is particularly useful for embryological studies because of the availability of tools to study and manipulate its embryonic development. Cupiennius is used to study axis formation, segmentation, appendage development, neurogenesis, and silk production. These studies contribute to our understanding of the evolution of these processes, but they also help us to understand the origin and diversification of evolutionary novelties. Comparisons between spiders and insects can show the degree of conservation and divergence of developmental mechanisms during arthropod evolution. Any embryological feature conserved between spiders and insects is likely to represent an ancestral feature for arthropods. Comparative molecular embryological work in insects and spiders should eventually allow us to define a molecular archetype for the phylum Arthropoda. This will be a necessary cornerstone for comparing the different metazoan phyla, including chordates. This protocol describes the detection of proliferating cells in whole-mount Cupiennius embryos. When labeled nucleotides are introduced into mitotically dividing cells, these cells incorporate the labels into the newly synthesized DNA. Thus, only cells that have synthesized DNA after the addition of the label will be detected. This protocol uses 5-bromo-2′-deoxy-uridine (BrdU) as a label that is subsequently detected by immunocytochemistry. BrdU labeling is a relatively easy way to detect cells that have recently synthesized DNA. The main advantage of this technique is that the label accumulates over time and, by varying the incubation time before fixation, an increasingly cumulative picture of cell proliferation activity can be obtained.
Dissecting Spider Embryos for Light Microscopy: Figure 1.
Authors: Prpic Nikola-Michael , Schoppmeier Michael , Damen Wim G.M.
Published: October 2008

INTRODUCTION

The spider Cupiennius salei, commonly known as the American wandering spider, is a particularly useful laboratory model for embryological studies because of the availability of tools to study and manipulate its embryonic development. Cupiennius is used to study axis formation, segmentation, appendage development, neurogenesis, and silk production. These studies contribute to our understanding of the evolution of these processes, but they also help us to understand the origin and diversification of evolutionary novelties. Comparisons between spiders and insects can show the degree of conservation and divergence of developmental mechanisms during arthropod evolution. Any embryological feature conserved between spiders and insects is likely to represent an ancestral feature for arthropods. Comparative molecular embryological work in insects and spiders should eventually allow us to define a molecular archetype for the phylum Arthropoda. This in itself will be a necessary cornerstone for comparing the different metazoan phyla, including chordates. Spider embryos can be studied as whole mounts under the dissection microscope. Alternatively, the embryos can be dissected and observed under the compound microscope. Preparing and dissecting spider embryos for compound microscopy is difficult due to the high amount of yolk, which makes the embryos very fragile. The following protocol describes how to make the necessary tools, then use them to obtain good preparations. Not all embryonic stages can be dissected and prepared; very young stages can only be examined as whole mounts.
Harvesting Monodelphis Embryos
Authors: Keyte Anna L. , Smith Kathleen K.
Published: October 2008

INTRODUCTION

Monodelphis domestica, the gray, short-tailed, or laboratory opossum, is the most commonly used laboratory marsupial. In addition to the factors that make it a convenient laboratory animal (small size, ease of care, nonseasonal breeding), it is the first marsupial whose genome has been sequenced. Monodelphis has proven useful as a model organism for studies on spinal cord regeneration, ultraviolet (UV)-induced melanoma, and genetic influences on cholesterol, as well as comparative studies of the immune system. In addition, Monodelphis has been used to understand the basic functions of the olfactory system and the role of various olfactory chemicals in social and reproductive behavior. Recently, Monodelphis has been used to understand fundamental aspects of marsupial development, anatomy, evolution, and evolutionary consequences of the derived marsupial mode of development and reproduction. Monodelphis embryos are easily harvested, as described in this protocol. Depending on the specific use for the embryo, there may be slight differences in euthanasia procedure, fixation, and embryo treatment. Most commonly, specimens will be used for anatomical or molecular (e.g., in situ hybridization) techniques, in which case they will be fixed in standard fixatives appropriate for the particular protocol.
Whole-Mount In Situ Hybridization in Monodelphis Embryos
Authors: Keyte Anna L. , Smith Kathleen K.
Published: October 2008

INTRODUCTION

Monodelphis domestica, the gray, short-tailed, or laboratory opossum, is the most commonly used laboratory marsupial. In addition to the factors that make it a convenient laboratory animal (small size, ease of care, nonseasonal breeding), it is the first marsupial whose genome has been sequenced. Monodelphis has proven useful as a model organism for studies on spinal cord regeneration, ultraviolet (UV)-induced melanoma, and genetic influences on cholesterol, as well as comparative studies of the immune system. In addition, Monodelphis has been used to understand the basic functions of the olfactory system and the role of various olfactory chemicals in social and reproductive behavior. Recently, Monodelphis has been used to understand fundamental aspects of marsupial development, anatomy, evolution, and evolutionary consequences of the derived marsupial mode of development and reproduction. This protocol details whole-mount in situ hybridization of Monodelphis embryos, but it is broadly applicable to any marsupial. Special conditions have been included throughout the protocol for various stages of marsupial embryos. Nevertheless, whole, preterm embryonic stages (~stage 33 to birth) have proven to be difficult to work with because formation of the cuticle prevents probe and antibody penetration.
Release of the Repressive Activity of Rice DELLA Protein SLR1 by Gibberellin Does Not Require SLR1 Degradation in the gid2 Mutant
Authors: Ueguchi-Tanaka Miyako , Hirano Ko , Hasegawa Yasuko , Kitano Hidemi , Matsuoka Makoto
Published: October 2008

The rice (Oryza sativa) DELLA protein SLR1 acts as a repressor of gibberellin (GA) signaling. GA perception by GID1 causes SLR1 protein degradation involving the F-box protein GID2; this triggers GA-associated responses such as shoot elongation and seed germination. In GA-insensitive and GA biosynthesis mutants, SLENDER RICE1 (SLR1) accumulates to high levels, and the severity of dwarfism is usually correlated with the level of SLR1 accumulation. An exception is the GA-insensitive F-box mutant gid2, which shows milder dwarfism than mutants such as gid1 and cps even though it accumulates higher levels of SLR1. The level of SLR1 protein in gid2 was decreased by loss of GID1 function or treatment with a GA biosynthesis inhibitor, and dwarfism was enhanced. Conversely, overproduction of GID1 or treatment with GA3 increased the SLR1 level in gid2 and reduced dwarfism. These results indicate that derepression of SLR1 repressive activity can be accomplished by GA and GID1 alone and does not require F-box (GID2) function. Evidence for GA signaling without GID2 was also provided by the expression behavior of GA-regulated genes such as GA-20oxidase1, GID1, and SLR1 in the gid2 mutant. Based on these observations, we propose a model for the release of GA suppression that does not require DELLA protein degradation.
Distribution and Evolution of Circular Miniproteins in Flowering Plants
Authors: Gruber Christian W. , Elliott Alysha G. , Ireland David C. , Delprete Piero G. , Dessein Steven , Göransson Ulf , Trabi Manuela , Wang Conan K. , Kinghorn Andrew B. , Robbrecht Elmar , Craik David J.
Published: October 2008

Cyclotides are disulfide-rich miniproteins with the unique structural features of a circular backbone and knotted arrangement of three conserved disulfide bonds. Cyclotides have been found only in two plant families: in every analyzed species of the violet family (Violaceae) and in few species of the coffee family (Rubiaceae). In this study, we analyzed >200 Rubiaceae species and confirmed the presence of cyclotides in 22 species. Additionally, we analyzed >140 species in related plant families to Rubiaceae and Violaceae and report the occurrence of cyclotides in the Apocynaceae. We further report new cyclotide sequences that provide insights into the mechanistic basis of cyclotide evolution. On the basis of the phylogeny of cyclotide-bearing plants and the analysis of cyclotide precursor gene sequences, we hypothesize that cyclotide evolution occurred independently in various plant families after the divergence of Asterids and Rosids (∼125 million years ago). This is strongly supported by recent findings on the in planta biosynthesis of cyclotides, which involves the serendipitous recruitment of ubiquitous proteolytic enzymes for cyclization. We further predict that the number of cyclotides within the Rubiaceae may exceed tens of thousands, potentially making cyclotides one of the largest protein families in the plant kingdom.
Interstitial cells of Cajal – their role in pacing and signal transmission in the digestive system
Authors: Hanani M. , Freund H.R.
Published: October 2008

Interstitial cells of Cajal (ICC) are located in most parts of the digestive system. Although they were discovered over 100 years ago, their function began to be unravelled only recently. Morphological observations have led to a number of hypotheses on the possible physiological roles of ICC: (1) these cells may be the source of slow electrical waves recorded in gastrointestinal (GI) muscles; (2) they participate in the conduction of electrical currents, and (3) mediate neural signals between enteric nerves and muscles. These hypotheses were supported by experiments in which the ICC‐containing layer was removed surgically, or when ICC were ablated chemically, and as a consequence the slow waves were absent. Electrophysiological experiments on isolated cells confirmed that ICC can generate rhythmic electrical activity and can also respond to messenger molecules known to be released from enteric nerves. In mice mutants deficient in ICC, or in mice treated with antibody against the protein c‐Kit, slow wave activity was impaired. These results support the role of ICC as pacemaker cells. Physiological studies have shown that ICC in certain GI regions are important for signal transmission between nerves and smooth muscle. There is evidence that pathological changes in ICC may be associated with GI motility disorders. The full interpretation of the role of ICC in disease conditions will require much further study on the physiology and pharmacology of these cells.
Glycinergic and GABAergic control of intensity‐response function of frog ERG waves under different conditions of light stimulation
Authors: Popova E.
Published: October 2008

The effect of glycinergic blockade by strychnine and GABAergic blockade by picrotoxin on the intensity‐response function and time course of ERG b‐ and d‐wave was investigated in dark and light adapted frog eyecups as well as in chromatically adapted eyecups, in which the responses were predominantly mediated by one photoreceptor type. Both of the blockers markedly increased the maximal response amplitude and thus increased the contrast gain of the mechanisms generating ERG waves. Strychnine but not picrotoxin narrowed the dynamic range of the b‐wave in all eyecups. The glycine and GABAergic control on retinal sensitivity however, depended on photoreceptor input. The b‐wave sensitivity was increased to the greatest extent when green rods mediated the response; it was slightly increased when the response was mediated by red cones and was not changed at all when red rods mediated the b‐wave. On the other hand the d‐wave sensitivity was enhanced regardless of photoreceptor input so that it became equal (dark) or even greater (light adapted eyes) than that of the b‐wave. Strychnine shortened but picrotoxin increased the implicit time of the b‐wave and both the blockers markedly slowed the d‐wave time course. Thus the blockers considerably diminished or fully eliminated the initial difference in time course between the ON and OFF response. The glycine‐ and GABAergic blockade did not principally alter the light adaptation process expressed in decreasing retinal sensitivity, narrowing the dynamic range and speeding the time course of the responses with increasing background illumination.
Endurance training in Wistar rats decreases receptor sensitivity to a serotonin agonist
Authors: Dwyer D. , Browning J.
Published: October 2008

There is mounting evidence that increased brain serotonin during exercise is associated with the onset of CNS‐mediated fatigue. Serotonin receptor sensitivity is likely to be an important determinant of this fatigue. Alterations in brain serotonin receptor sensitivity were examined in Wistar rats throughout 6 weeks of endurance training, running on a treadmill four times a week with two exercise tests per week to exhaustion. Receptor sensitivity was determined indirectly as the reduction in exercise time in response to a dose of a serotonin (1A) agonist, m‐chlorophenylpiperazine (m‐CPP). The two groups of controls were used to examine (i) the effect of the injectionper seon exercise performance and (ii) changes in serotonin receptor sensitivity associated with maturation. In the test group, undrugged exercise performance significantly improved by 47% after 6 weeks of training (4518 ± 729 to 6640 ± 903 s,P=0.01). Drugged exercise performance also increased significantly from week 1 to week 6 (306 ± 69–712 ± 192 s,P = 0.04). Control group results indicated that the dose of m‐CPP alone caused fatigue during exercise tests and that maturation was not responsible for any decrease in receptor sensitivity. Improved resistance to the fatiguing effects of the serotonin agonist suggests desensitization of central serotonin receptors, probably the 5‐HT1A receptors. Endurance training appears to stimulate an adaptive response to the fatiguing effects of increased brain serotonin, which may enhance endurance exercise performance.
Distribution of Palaeozoic reworking in the Western Arunta Region and northwestern Amadeus Basin from40Ar/39Ar thermochronology: implications for the evolution of intracratonic basins
Authors: McLaren Sandra , Sandiford Mike , Dunlap W. James , Scrimgeour Ian , Close Dorothy , Edgoose Christine
Published: October 2008

The Centralian Superbasin in central Australia is one of the most extensive intracratonic basins known from a stable continental setting, but the factors controlling its formation and subsequent structural dismemberment continue to be debated. Argon thermochronology of K‐feldspar, sensitive to a broad range of temperatures (∼150 to 350 °C), provides evidence for the former extent and thickness of the superbasin and points toward thickening of the superbasin succession over the now exhumed Arunta Region basement. These data suggest that before Palaeozoic tectonism, there was around 5–6 km of sediment present over what is now the northern margin of the Amadeus Basin, and, if the Centralian superbasin was continuous, between 6 and 8 km over the now exhumed basement.40Ar/39Ar data from neoformed fine‐grained muscovite suggests that Palaeozoic deformation and new mineral growth occurred during the earliest compressional phase of the Alice Springs Orogeny (ASO) (440–375 Ma) and was restricted to shear zones. Significantly, several shear zones active during the late Mesoproterozoic Teapot Orogeny were not reactivated at this time, suggesting that the presence of pre‐existing structures was not the only controlling factor in localizing Palaeozoic deformation. A range of Palaeozoic ages of 440–300 Ma from samples within and external to shear zones points to thermal disturbance from at least the early Silurian through until the late Carboniferous and suggests final cooling and exhumation of the terrane in this interval. The absence of evidence for active deformation and/or new mineral growth in the late stages of the ASO (350–300 Ma) is consistent with a change in orogenic dynamics from thick‐skinned regionally extensive deformation to a more restricted localized high‐geothermal gradient event.
Functional implications of temperature‐correlated colour polymorphism in an iridescent, scarabaeine dung beetle
Authors: DAVIS ADRIAN L.V. , BRINK D. JOHAN , SCHOLTZ CLARKE H. , PRINSLOO LINDA C. , DESCHODT CHRISTIAN M.
Published: October 2008

Abstract1. In many Coleoptera, iridescent colouration is generated by exoskeleton ultra‐structure, within which multilayer interference reflects only certain wavelengths. Published work indicates that the colour polymorphism shown by some iridescent beetles is under genetic control. However, the present study suggests environmental involvement in the polymorphic southern African dung beetle,Gymnopleurus humanusMacleay.

2. At 24 study sites across a 1000‐km latitudinal temperature gradient, population samples ofG. humanuswere dominated by blue individuals in the cooler south, by cupreous individuals in the warmer north, and by locally co‐occurring blue, green and cupreous individuals in intermediate situations.

3. Using digital reflectance spectrophotometry, we measured wavelength intensity values across the visible spectrum (400–800 nm) and used the 70 measured specimens to estimate maximum reflectance from a further 3912 beetles. Differences in mean reflectance values between 24 populations were strongly correlated with average annual temperatures at study sites.

4. Much stronger correlations between mean reflectance values and average temperatures of the cool dry season months suggest that the cross‐climatic patterns may be related to interaction between breeding seasonality and development under different cooler temperatures.

5. Published evidence suggests that inherent physical properties of cholesteric liquid crystals and their responses to different thermal conditions could, potentially, generate the different exocuticle ultra‐structure responsible for different reflected colour wavelengths. Furthermore, colour polymorphism could be advantageous across a gradient from cooler to warmer climate as a result of the different thermal properties of different colours.

6. Given the correlation with temperature, it is predicted that the prevailing reflected colour balance in southern populations would shift in response to global climatic change.