bluuebunny/crossref_metadata_2025 huggingface dataset:
The Drosophila nuclear factor DREF positively regulates the expression of the mitochondrial transcription termination factor DmTTF
Authors: Fernández-Moreno Miguel Á. , Bruni Francesco , Adán Cristina , Sierra Rosana HERNÁNDEZ , Polosa Paola LOGUERCIO , Cantatore Palmiro , Garesse Rafael , Roberti Marina
Published: November 2008

The DREF [DRE (DNA replication-related element)-binding factor], which regulates the transcription of a group of cell proliferation-related genes in Drosophila, also controls the expression of three genes involved in mtDNA (mitochondrial DNA) replication and maintenance. In the present study, by in silico analysis, we have identified DREs in the promoter region of a gene participating in mtDNA transcription, the DmTTF (Drosophila mitochondrial transcription termination factor). Transient transfection assays in Drosophila S2 cells, with mutated versions of DmTTF promoter region, showed that DREs control DmTTF transcription; moreover, gel-shift and ChIP (chromatin immunoprecipitation) assays demonstrated that the analysed DRE sites interact with DREF in vitro and in vivo. Accordingly, DREF knock-down in S2 cells by RNAi (RNA interference) induced a considerable decrease in DmTTF mRNA level. These results clearly demonstrate that DREF positively controls DmTTF expression. On the other hand, mtRNApol (mitochondrial RNA polymerase) lacks DREs in its promoter and is not regulated in vivo by DREF. In situ RNA hybridization studies showed that DmTTF was transcribed almost ubiquitously throughout all stages of Drosophila embryogenesis, whereas mtRNApol was efficiently transcribed from stages 11–12. Territories where transcription occurred mostly were the gut and Malpighi tubes for DmTTF, and the gut, mesoderm, pharyngeal muscle and Malpighi tubes for mtRNApol. The partial overlapping in the temporal and spatial mRNA expression patterns confirms that transcription of the two genes is differentially regulated during embryogenesis and suggests that DmTTF might play multiple roles in the mtDNA transcription process, for which different levels of the protein with respect to mtRNApol are required.
Design of a polypeptide FRET substrate that facilitates study of the antimicrobial protease lysostaphin
Authors: Bardelang Philip , Vankemmelbeke Mireille , Zhang Ying , Jarvis Hannah , Antoniadou Eleni , Rochette Sophie , Thomas Neil R. , Penfold Christopher N. , James Richard
Published: November 2008

We have developed a polypeptide lysostaphin FRET (fluorescence resonance energy transfer) substrate (MV11F) for the endopeptidase activity of lysostaphin. Site-directed mutants of lysostaphin that abolished the killing activity against Staphylococcus aureus also completely inhibited the endopeptidase activity against the MV11 FRET substrate. Lysostaphin-producing staphylococci are resistant to killing by lysostaphin through incorporation of serine residues at positions 3 and 5 of the pentaglycine cross-bridge in their cell walls. The MV11 FRET substrate was engineered to introduce a serine residue at each of four positions of the pentaglycine target site and it was found that only a serine residue at position 3 completely inhibited cleavage. The introduction of random, natural amino acid substitutions at position 3 of the pentaglycine target site demonstrated that only a glycine residue at this position was compatible with lysostaphin cleavage of the MV11 FRET substrate. A second series of polypeptide substrates (decoys) was developed with the GFP (green fluorescent protein) domain of MV11 replaced with that of the DNase domain of colicin E9. Using a competition FRET assay, the lysostaphin endopeptidase was shown to bind to a decoy peptide containing a GGSGG cleavage site. The MV11 substrate provides a valuable system to facilitate structure/function studies of the endopeptidase activity of lysostaphin and its orthologues.
Monte Carlo simulations of amphiphilic nanoparticle self-assembly
Authors: Davis Jonathan R. , Panagiotopoulos Athanassios Z.
Published: November 2008

Grand canonical Monte Carlo simulations on a cubic lattice are used to examine aggregation and phase separation of model amphiphiles with bulky head groups. The amphiphiles studied consist of a rigid, roughly spherical nanoparticle attached to one or more flexible chains. Overlapping distributions of energy and density are combined via histogram reweighting to obtain the free energy and osmotic pressure as a function of temperature and concentration. Finite size effects are used to distinguish between first order transitions to a disordered liquid or lamellar phase and continuous transitions to micelles. The transition type depends on the relative size of the solvophobic and neutral portions of the amphiphiles; none of the systems studied here exhibit both types of transition. The critical micellar concentration increases with temperature over the range of conditions examined. Solvophobic nanoparticles with neutral chains phase separate when the attached chain is short and form micelles for longer attached chains. For structures with neutral nanoparticles and solvophobic chains, amphiphile geometry plays a key role in determining whether the micelles that form are spheres or flat bilayers. Nanoparticles with many chains tend to form flat bilayers, while those with only one or two chains form nearly spherical aggregates. Particles with long chains undergo macroscopic phase separation instead of micellization, and the temperature range over which the first order transition occurs depends on the total volume occupied by the solvophobic segments.
Nanometric size effect on Ge diffusion in polycrystalline Si
Authors: Portavoce A. , Chai G. , Chow L. , Bernardini J.
Published: November 2008

The nanosize effect on Ge diffusion (850≤T≤1000 °C) in polycrystalline Si layers is investigated. The Ge diffusion coefficients in microcrystalline and nanocrystalline Si layers made of 30 μm and 40 nm wide grains, respectively, are measured and compared. In the microcrystalline Si layer, the Ge diffusion coefficient in micrograin boundaries is measured using a conventional analytical solution of Fick’s equations corresponding to the Fisher model. In the nanocrystalline Si layer, the Ge diffusion coefficients in nanograins and in nanograin boundaries are measured via a method based on two-dimensional simulations using the Fisher model geometry. The diffusivities in nanograins and nanograin boundaries are one order of magnitude higher than in micrograins and micrograin boundaries, respectively. However, the nanosize effect appears to be different in grains and grain boundaries; despite that the activation energy for diffusion in 40 nm wide grains is at least 1 eV lower than in Si bulk. The activation energy in nanograin boundaries is about the same as in micrograin boundaries.
On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters. II. The water hexamer and van der Waals interactions
Authors: Santra Biswajit , Michaelides Angelos , Fuchs Martin , Tkatchenko Alexandre , Filippi Claudia , Scheffler Matthias
Published: November 2008

Second order Møller–Plesset perturbation theory at the complete basis set limit and diffusion quantum Monte Carlo are used to examine several low energy isomers of the water hexamer. Both approaches predict the so-called prism to be the lowest energy isomer, followed by cage, book, and cyclic isomers. The energies of the four isomers are very similar, all being within 10–15 meV/H2O. These reference data are then used to evaluate the performance of several density-functional theory exchange-correlation (xc) functionals. A subset of the xc functionals tested for smaller water clusters [I. Santra et al., J. Chem. Phys. 127, 184104 (2007)] has been considered. While certain functionals do a reasonable job at predicting the absolute dissociation energies of the various isomers (coming within 10–20 meV/H2O), none predict the correct energetic ordering of the four isomers nor does any predict the correct low total energy isomer. All xc functionals tested either predict the book or cyclic isomers to have the largest dissociation energies. A many-body decomposition of the total interaction energies within the hexamers leads to the conclusion that the failure lies in the poor description of van der Waals (dispersion) forces in the xc functionals considered. It is shown that the addition of an empirical pairwise (attractive) C6R−6 correction to certain functionals allows for an improved energetic ordering of the hexamers. The relevance of these results to density-functional simulations of liquid water is also briefly discussed.
Integration of vertical InAs nanowire arrays on insulator-on-silicon for electrical isolation
Authors: Dayeh Shadi A. , Chen Peng , Jing Yi , Yu Edward T. , Lau S. S. , Wang Deli
Published: November 2008

Vertical and electrically isolated InAs nanowires (NWs) are integrated with Si in a technique that bypasses structural defects and transport barriers at the Si–III–V NW interface. Smart-cut® technique is used to transfer a thin InAs layer onto SiO2/Si and is subsequently used for ordered organometallic vapor phase epitaxy of InAs NWs. The InAs layer in the regions between the InAs NWs is etched resulting in ordered, vertical, and electrically isolated InAs NW arrays. This transfer and fabrication technique enables heteroepitaxy of three dimensional III–V structures on Si and allows the realization of vertical devices with unprecedented control over their architectures.
Enhancing single-molecule photostability by optical feedback from quantum jump detection
Authors: Jacques V. , Murray J. D. , Marquier F. , Chauvat D. , Grosshans F. , Treussart F. , Roch J.-F.
Published: November 2008

We report an optical technique that yields an enhancement of single-molecule photostability by greatly suppressing photobleaching pathways which involve photoexcitation from the triplet state. This is accomplished by dynamically switching off the excitation laser when a quantum jump of the molecule to the triplet state is optically detected. The resulting improvement in photostability unambiguously confirms the importance of photoexcitation from the triplet state in photobleaching dynamics and will allow the investigation of new phenomena at the single-molecule level.
First-principles studies of water adsorption on graphene: The role of the substrate
Authors: Wehling Tim O. , Lichtenstein Alexander I. , Katsnelson Mikhail I.
Published: November 2008

We investigate the electronic properties of graphene upon water adsorption and study the influence of the SiO2 substrate in this context using density functional calculations. Perfect suspended graphene is rather insensitive to H2O adsorbates, as doping requires highly oriented H2O clusters. For graphene on a defective SiO2 substrate, we find a strongly different behavior: H2O adsorbates can shift the substrate’s impurity bands and change their hybridization with the graphene bands. In this way, H2O can lead to doping of graphene for much lower adsorbate concentrations than for free hanged graphene. The effect depends strongly on the microscopic substrate properties.
Current collapse in AlGaN/GaN transistors studied using time-resolved Raman thermography
Authors: Simms R. J. T. , Pomeroy J. W. , Uren M. J. , Martin T. , Kuball M.
Published: November 2008

Current collapse in AlGaN/GaN high electron mobility transistors was investigated using time-resolved Raman thermography. The virtual-gate mechanism was visualized by changes in the device temperature distribution, illustrating an effective gate lengthening up to 0.6 um. Two devices with different levels of current collapse are compared, demonstrating that the effective gate length increases for greater current collapse. A comparison of two-dimensional drift diffusion simulations with experimental data was used to estimate a lower limit for the charge trapping density in the virtual-gate region. This was found to be of the order of 2×1013 cm−2 for a device exhibiting relatively little current collapse.
A Geodemographic Profiler for High Offender Propensity Areas in the City of Tshwane, South Africa
Authors: Breetzke Gregory D , Horn Andre C
Published: November 2008

Postapartheid South Africa has been plagued by an increase in crime across all categories. While a significant amount of criminological research has been undertaken in the country, the spatial analysis of crime and offenders, a basic prerequisite for a functional crime management strategy, has not been adequately addressed at a sufficiently fine scale of aggregation. This paper reports on the geodemographic development of offender risk profiles for neighbourhoods in the City of Tshwane Metropolitan Municipality in South Africa. Geodemographics is a relatively new geo-analytical technique that is being increasingly used in policing applications to complement law enforcement techniques and provide further insight into offenders and their offences. Findings of the study indicate that neighbourhoods at a high risk for offender development are amongst the most socially and economically deprived in the municipality and are disproportionately occupied by black Africans. The results highlight a need to reassess the current law enforcement approach to crime reduction in the country and return to the crime prevention initiatives that were part of the National Crime Prevention Strategy of the 1990s.
Selective benefits of damage partitioning in unicellular systems and its effects on aging
Authors: Erjavec N. , Cvijovic M. , Klipp E. , Nyström T.
Published: November 2008

Cytokinesis in unicellular organisms sometimes entails a division of labor between cells leading to lineage-specific aging. To investigate the potential benefits of asymmetrical cytokinesis, we created a mathematical model to simulate the robustness and fitness of dividing systems displaying different degrees of damage segregation and size asymmetries. The model suggests that systems dividing asymmetrically (size-wise) or displaying damage segregation can withstand higher degrees of damage before entering clonal senescence. When considering population fitness, a system producing different-sized progeny like budding yeast is predicted to benefit from damage retention only at high damage propagation rates. In contrast, the fitness of a system of equal-sized progeny is enhanced by damage segregation regardless of damage propagation rates, suggesting that damage partitioning may also provide an evolutionary advantage in systems dividing by binary fission. Indeed, by using
Schizosaccharomyces pombe
as a model, we experimentally demonstrate that damaged proteins are unevenly partitioned during cytokinesis and the damage-enriched sibling suffers from a prolonged generation time and accelerated aging. This damage retention in
S. pombe
is, like in
Saccharomyces cerevisiae
, Sir2p- and cytoskeleton-dependent, suggesting this to be an evolutionarily conserved mechanism. We suggest that sibling-specific aging may be a result of the strong selective advantage of damage segregation, which may be more common in nature than previously anticipated.
A bifunctional kinase-phosphatase in bacterial chemotaxis
Authors: Porter Steven L. , Roberts Mark A. J. , Manning Cerys S. , Armitage Judith P.
Published: November 2008

Phosphorylation-based signaling pathways employ dephosphorylation mechanisms for signal termination. Histidine to aspartate phosphosignaling in the two-component system that controls bacterial chemotaxis has been studied extensively.
Rhodobacter sphaeroides
has a complex chemosensory pathway with multiple homologues of the
Escherichia coli
chemosensory proteins, although it lacks homologues of known signal-terminating CheY-P phosphatases, such as CheZ, CheC, FliY or CheX. Here, we demonstrate that an unusual CheA homologue, CheA
3
, is not only a phosphodonor for the principal CheY protein, CheY
6
, but is also is a specific phosphatase for CheY
6
-P. This phosphatase activity accelerates CheY
6
-P dephosphorylation to a rate that is comparable with the measured stimulus response time of approximately 1 s. CheA
3
possesses only two of the five domains found in classical CheAs, the Hpt (P1) and regulatory (P5) domains, which are joined by a 794-amino acid sequence that is required for phosphatase activity. The P1 domain of CheA
3
is phosphorylated by CheA
4
, and it subsequently acts as a phosphodonor for the response regulators. A CheA
3
mutant protein without the 794-amino acid region lacked phosphatase activity, retained phosphotransfer function, but did not support chemotaxis, suggesting that the phosphatase activity may be required for chemotaxis. Using a nested deletion approach, we showed that a 200-amino acid segment of CheA
3
is required for phosphatase activity. The phosphatase activity of previously identified nonhybrid histidine protein kinases depends on the dimerization and histidine phosphorylation (DHp) domains. However, CheA
3
lacks a DHp domain, suggesting that its phosphatase mechanism is different from that of other histidine protein kinases.
A mutant GlnD nitrogen sensor protein leads to a nitrogen-fixing but ineffective
Sinorhizobium meliloti
symbiosis with alfalfa
Authors: Yurgel Svetlana N. , Kahn Michael L.
Published: November 2008

The nitrogen-fixing symbiosis between rhizobia and legume plants is a model of coevolved nutritional complementation. The plants reduce atmospheric CO
2
by photosynthesis and provide carbon compounds to symbiotically associated bacteria; the rhizobia use these compounds to reduce (fix) atmospheric N
2
to ammonia, a form of nitrogen the plants can use. A key feature of symbiotic N
2
fixation is that N
2
fixation is uncoupled from bacterial nitrogen stress metabolism so that the rhizobia generate “excess” ammonia and release this ammonia to the plant. In the symbiosis between
Sinorhizobium meliloti
and alfalfa, mutations in GlnD, the major bacterial nitrogen stress response sensor protein, led to a symbiosis in which nitrogen was fixed (Fix
+
) but was not effective (Eff
−
) in substantially increasing plant growth. Fixed
15
N
2
was transported to the shoots, but most fixed
15
N was not present in the plant after 24 h. Analysis of free-living
S. meliloti
strains with mutations in genes related to nitrogen stress response regulation (
glnD
,
glnB
,
ntrC
, and
ntrA
) showed that catabolism of various nitrogen-containing compounds depended on the NtrC and GlnD components of the nitrogen stress response cascade. However, only mutants of GlnD with an amino terminal deletion had the unusual Fix
+
Eff
−
symbiotic phenotype, and the data suggest that these
glnD
mutants export fixed nitrogen in a form that the plants cannot use. These results indicate that bacterial nitrogen stress regulation is important to symbiotic productivity and suggest that GlnD may act in a novel way to influence symbiotic behavior.
Leptin-enhanced neointimal hyperplasia is reduced by mTOR and PI3K inhibitors
Authors: Shan Jian , Nguyen Thomas B. , Totary-Jain Hana , Dansky Hayes , Marx Steven O. , Marks Andrew R.
Published: November 2008

Despite the use of the sirolimus (rapamycin) drug-eluting coronary stent, diabetics are at increased risk of developing in-stent restenosis for unclear reasons. Hyperleptinemia, which often coexists with diabetes and metabolic syndrome, is an independent risk factor for progression of coronary artery disease. It has not been determined whether elevated circulating leptin decreases the efficacy of the sirolimus drug-eluting stent in inhibiting neointimal hyperplasia, the process underlying restenosis after stenting. Here we show that leptin activates the mammalian target of rapamycin (mTOR) signaling pathway in primary murine vascular smooth muscle cells (VSMC) and stimulates VSMC proliferation in a PI3K-dependent fashion. Exogenous leptin, administered at levels comparable to those found in obese humans, promotes neointimal VSMC hyperplasia in a murine femoral artery wire injury model. Leptin significantly increases the dose of the mTOR inhibitor sirolimus that is required for effective inhibition of neointimal formation. Combination therapy with LY294002, a PI3K inhibitor, and sirolimus effectively inhibits leptin-enhanced neointimal hyperplasia. These data show that, in the setting of hyperleptinemia, higher doses of an mTOR inhibitor, or combination therapy with mTOR and PI3K inhibitors, inhibits neointimal hyperplasia after arterial injury. These studies may explain the higher rates of restenosis observed in diabetics treated with a sirolimus-eluting coronary stent and suggest a potential novel therapeutic approach for inhibiting in-stent restenosis in such patients.
Restoration of electron transport without proton pumping in mammalian mitochondria
Authors: Perales-Clemente Ester , Bayona-Bafaluy Maria Pilar , Pérez-Martos Acisclo , Barrientos Antoni , Fernández-Silva Patricio , Enriquez Jose Antonio
Published: November 2008

We have restored the CoQ oxidative capacity of mouse mtDNA-less cells (ρ° cells) by transforming them with the alternative oxidase
Aox
of
Emericella nidulans
. Cotransforming ρ° cells with the NADH dehydrogenase of
Saccharomyces cerevisiae
,
Ndi1
and
Aox
recovered the NADH DH/CoQ reductase and the CoQ oxidase activities. CoQ oxidation by AOX reduces the dependence of ρ° cells on pyruvate and uridine. Coexpression of AOX and NDI1 further improves the recycling of NAD
+
. Therefore, 2 single-protein enzymes restore the electron transport in mammalian mitochondria substituting >80 nuclear DNA-encoded and 11 mtDNA-encoded proteins. Because those enzymes do not pump protons, we were able to split electron transport and proton pumping (ATP synthesis) and inquire which of the metabolic deficiencies associated with the loss of oxidative phosphorylation should be attributed to each of the 2 processes.
Toxoplasma gondiiinfection blocks the development of allergic airway inflammation in BALB/c mice
Authors: Fenoy I , Giovannoni M , Batalla E , Martin V , Frank F M , Piazzon I , Goldman A
Published: November 2008

There is a link between increased allergy and a reduction of some infections in western countries. Epidemiological data also show that respiratory allergy is less frequent in people exposed to orofaecal and foodborne microbes such as Toxoplasma gondii. Infection with T. gondii induces a strong cell-mediated immunity with a highly polarized T helper type 1 (Th1) response in early stages of infection. Using a well-known murine model of allergic lung inflammation, we sought to investigate whether T. gondii infection could modulate the susceptibility to develop respiratory allergies. Both acute and chronic infection with T. gondii before allergic sensitization resulted in a diminished allergic inflammation, as shown by a decrease in bronchoalveolar lavage (BAL) eosinophilia, mononuclear and eosinophil cell infiltration around airways and vessels and goblet cell hyperplasia. Low allergen-specific immunoglobulin (Ig)E and IgG1 and high levels of allergen-specific IgG2a serum antibodies were detected. A decreased interleukin (IL)-4 and IL-5 production by lymph node cells was observed, while no antigen-specific interferon-γ increase was detected. Higher levels of the regulatory cytokine IL-10 were found in BAL from infected mice. These results show that both acute and chronic parasite infection substantially blocked development of airway inflammation in adult BALB/c mice. Our results support the hypothesis that T. gondii infection contributes to protection against allergy in humans.
Diverse T‐cell differentiation potentials of human fetal thymus, fetal liver, cord blood and adult bone marrow CD34 cells on lentiviral Delta‐like‐1‐modified mouse stromal cells
Authors: Patel Ekta , Wang Bei , Lien Lily , Wang Yichen , Yang Li‐Jun , Moreb Jan S. , Chang Lung‐Ji
Published: November 2008

Human haematopoietic progenitor/stem cells (HPCs) differentiate into functional T cells in the thymus through a series of checkpoints. A convenient in vitro system will greatly facilitate the understanding of T‐cell development and future engineering of therapeutic T cells. In this report, we established a lentiviral vector‐engineered stromal cell line (LSC) expressing the key lymphopoiesis regulator Notch ligand, Delta‐like 1 (DL1), as feeder cells (LSC‐mDL1) supplemented with Flt3 ligand (fms‐like tyrosine kinase 3, Flt3L or FL) and interleukin‐7 for the development of T cells from CD34+ HPCs. We demonstrated T‐cell development from human HPCs with various origins including fetal thymus (FT), fetal liver (FL), cord blood (CB) and adult bone marrow (BM). The CD34+ HPCs from FT, FL and adult BM expanded more than 100‐fold before reaching the β‐selection and CD4/CD8 double‐positive T‐cell stage. The CB HPCs, on the other hand, expanded more than 1000‐fold before β‐selection. Furthermore, the time required to reach β‐selection differed for the various HPCs, 7 days for FT, 14 days for FL and CB, and 35 days for adult BM. Nevertheless, all of the T cells developed in vitro were stalled at the double‐positive or immature single‐positive stage with the exception that some CB‐derived T cells arrived at a positive selection stage. Consequently, the LSC‐mDL1 culture system illustrated diverse T‐cell development potentials of pre‐ and post‐natal and adult human BM HPCs. However, further modification of this in vitro T‐cell development system is necessary to attain fully functional T cells.
T‐cell receptor binding affinities and kinetics: impact on T‐cell activity and specificity
Authors: Stone Jennifer D. , Chervin Adam S. , Kranz David M.
Published: November 2008

The interaction between the T‐cell receptor (TCR) and its peptide–major histocompatibility complex (pepMHC) ligand plays a critical role in determining the activity and specificity of the T cell. The binding properties associated with these interactions have now been studied in many systems, providing a framework for a mechanistic understanding of the initial events that govern T‐cell function. There have been various other reviews that have described the structural and biochemical features of TCR : pepMHC interactions. Here we provide an overview of four areas that directly impact our understanding of T‐cell function, as viewed from the perspective of the TCR : pepMHC interaction: (1) relationships between T‐cell activity and TCR : pepMHC binding parameters, (2) TCR affinity, avidity and clustering, (3) influence of coreceptors on pepMHC binding by TCRs and T‐cell activity, and (4) impact of TCR binding affinity on antigenic peptide specificity.
A discussion of different types of glacial refugia used in mountain biogeography and phylogeography
Authors: Holderegger Rolf , Thiel‐Egenter Conny
Published: November 2008

With the recent rise of phylogeography, the biogeography of mountain species (species with their current main distribution above timber line), especially their glacial history, has attracted renewed interest. In particular, the question of where mountain species survived the ice ages has been approached in many phylogeographical studies. The terminology of glacial refugia of mountain species is often confusing, contradictory or counter‐intuitive. Our aim is to clarify and simplify this terminology. First, we offer a general definition of the term glacial refugium for mountain species. Then, we discuss three main types of glacial refugia of mountain species, i.e. nunatak, peripheral and lowland refugia. We believe that the discrimination of these three types of glacial refugia is sufficient to describe the glacial survival of (most) mountain species. Finally, we argue that the terms in situ survival and ex situ survival and the term periglacial refugium should only be used to describe specific cases of glacial history. No simple classification system can adequately describe every kind of glacial refugium, but we propose that authors should focus on providing comprehensive descriptions of particular refugial situations instead of introducing new terminology.
Population genetics of Galápagos land iguana (genus Conolophus) remnant populations
Authors: TZIKA ATHANASIA C. , ROSA SABRINA F. P. , FABIANI ANNA , SNELL HOWARD L. , SNELL HEIDI M. , MARQUEZ CRUZ , TAPIA WASHINGTON , RASSMANN KORNELIA , GENTILE GABRIELE , MILINKOVITCH MICHEL C.
Published: November 2008

The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive‐bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species‐specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile.
The roles of allopatric divergence and natural selection in quantitative trait variation across a secondary contact zone in the lizard Anolis roquet
Authors: JOHANSSON HELENA , SURGET‐GROBA YANN , THORPE ROGER S.
Published: November 2008

Populations of the Caribbean lizard, Anolis roquet, are thought to have experienced long periods of allopatry before recent secondary contact. To elucidate the effects of past allopatry on population divergence in A. roquet, we surveyed parallel transects across a secondary contact zone in northeastern Martinique. We used diagnostic molecular mitochondrial DNA markers to test fine‐scale association of mitochondrial DNA lineage and geological region, multivariate statistical techniques to explore quantitative trait pattern, and cline fitting techniques to model trait variation across the zone of secondary contact. We found that lineages were strongly associated with geological regions along both transects, but quantitative trait patterns were remarkably different. Patterns of morphological and mitochondrial DNA variation were consistent with a strong barrier to gene flow on the coast, whereas there were no indications of barriers to gene flow in the transitional forest. Hence, the coastal populations behaved as would be predicted by an allopatric model of divergence in this complex, while those in the transitional forest did not, despite the close proximity of the transects and their shared geological history. Patterns of geographical variation in this species complex, together with environmental data, suggest that on balance, selection regimes on either side of the secondary contact zone in the transitional forest may be more convergent, while those either side of the secondary contact zone on the coast are more divergent. Hence, the evolutionary consequences of allopatry may be strongly influenced by local natural selection regimes.
Revealing the hidden complexities of mtDNA inheritance
Authors: WHITE DANIEL JAMES , WOLFF JONCI NIKOLAI , PIERSON MELANIE , GEMMELL NEIL JOHN
Published: November 2008

Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re‐evaluated, and we assess the implications of these new‐found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses.
Drastic post‐LGM expansion and lack of historical genetic structure of a subtropical fig‐pollinating wasp (Ceratosolensp. 1) ofFicus septicain Taiwan
Authors: LIN RONG‐CHIEN , YEUNG CAROL K‐L. , LI SHOU‐HSIEN
Published: November 2008

The climatic oscillations of the last glacial period have had profound influences on the demography and levels of genetic diversity of extant species. Molecular evidence of glacial effects on temperate species has been well documented, whereas little is known regarding that on subtropical species. Here we present analyses based on partial sequences of the mitochondrial cytochromecoxidase subunit I (COI) gene (1052 bp) and genotypes at 15 microsatellite loci to investigate the historical demography, population structure and ongoing gene flow of an undescribed fig‐pollinating wasp (Ceratosolensp. 1) ofFicus septicain subtropical Taiwan. Reconstructed historical demography based on the coalescent tree ofCOIsequences suggests thatC. sp. 1 has undergone a drastic population expansion which was tightly coupled with climatic changes since the last glacial maximum (LGM). The magnitude of the population size change was approximately 500‐fold, indicating that the population of this wasp and its host was likely highly compressed during the last glacial period. The lack of significant population differentiation (FST < 0.02, for all pairwiseFSTvalues) may be due to rapid postglacial expansion facilitated by long‐distance dispersal, although a low frequency of first‐generation migrants was detected. Our results clearly demonstrate how recent climatic changes since the LGM and dispersal ability have jointly shaped the genetic composition of a subtropical fig‐pollinating wasp.
Using patterns of genetic structure based on microsatellite loci to test hypotheses of current hybridization, ancient hybridization and incomplete lineage sorting in Conradina (Lamiaceae)
Authors: EDWARDS C. E. , SOLTIS D. E. , SOLTIS P. S.
Published: November 2008

Hybridization and/or incomplete sorting of ancestral polymorphism are commonly implicated to explain discordant phylogenetic analyses of closely related species complexes. One genus in which these phenomena have been suggested to have played major roles based on phylogenetic data is Conradina, a genus of mints (Lamiaceae) endemic to the southeastern USA containing several endangered species. The goals of this study were to use microsatellite data to better understand patterns of genetic structure in Conradina, to test hypotheses of recent or ancient hybridization and incomplete lineage sorting, and to clarify species boundaries. Individuals from 55 populations representing all Conradina species were genotyped using 10 microsatellite loci. Analyses of the patterns of genetic structure in Conradina revealed a clear differentiation of populations following recognized species boundaries, indicating that species have diverged from one another genetically and interspecific hybridization has not occurred recently. Neither ancient hybridization nor incomplete lineage sorting is supported as the sole cause of species nonmonophyly, suggesting that both may have contributed to patterns found in phylogenetic trees; however, analyses of other types of data may be more appropriate to distinguish between these two hypotheses. Because all described species appear to be valid entities, the current listing status of most endangered species of Conradina is appropriate; however, populations of Conradina canescens are genetically differentiated into three groups, each of which may merit species status, and several recently discovered populations of Conradina in Dunn's Creek State Park in Florida are highly differentiated genetically and also appear to represent a new species.
Histone deacetylation is required for progression through mitosis in tobacco cells
Authors: Li Yan , Butenko Yana , Grafi Gideon
Published: November 2008

Post‐translational modifications of core histone proteins play a key role in chromatin structure and function. Here, we study histone post‐translational modifications during reentry of protoplasts derived from tobacco mesophyll cells into the cell cycle and evaluate their significance for progression through mitosis. Methylation of histone H3 at lysine residues 4 and 9 persisted in chromosomes during all phases of the cell cycle. However, acetylation of H4 and H3 was dramatically reduced during mitosis in a stage‐specific manner; while deacetylation of histone H4 commenced at prophase and persisted up to telophase, histone H3 remained acetylated up to metaphase but was deacetylated at anaphase and telophase. Phosphorylation of histone H3 at serine 10 was initiated at prophase, concomitantly with deacetylation of histone H4, and persisted up to telophase. Preventing histone deacetylation by the histone deacetylase inhibitor trichostatin A (TSA) led to accumulation of protoplasts at metaphase–anaphase, and reduced S10 phosphorylation during anaphase and telophase; in cultured tobacco cells, TSA significantly reduced the frequency of mitotic figures. Our results indicate that deacetylation of histone H4 and H3 in tobacco protoplasts occurs during mitosis in a phase‐specific manner, and is important for progression through mitosis.
EGY1 encodes a membrane‐associated and ATP‐independent metalloprotease that is required for chloroplast development
Authors: Chen Gu , Bi Yu Rong , Li Ning
Published: November 2008

Chloroplast development requires coordinated expression of both nuclear‐ and chloroplast‐encoded genes. To better understand the roles played by nuclear‐encoded chloroplast proteins in chloroplast biogenesis, we isolated an Arabidopsis mutant, egy1‐1, which has a dual phenotype, reduced chlorophyll accumulation and abnormal hypocotyl gravicurvature. Subsequent map‐based cloning and DNA sequencing of the mutant gene revealed a 10‐bp deletion in an EGY1 gene, which encodes a 59‐kDa metalloprotease that contains eight trans‐membrane domains at its C‐terminus, and carries out β‐casein degradation in an ATP‐independent manner. EGY1 protein accumulation varies between tissue types, being most prominent in leaf and stem tissues, and is responsive to light and ethylene. EGY1‐GFP hybrid proteins are localized in the chloroplast. egy1 mutant chloroplasts had reduced granal thylakoids and poorly developed lamellae networks. Furthermore, the accumulation of chlorophyll a/b binding proteins of the light‐harvesting complexes I and II (Lhca and Lhcb) are significantly decreased in three separate loss‐of‐function egy1 mutants. Taken together, these results suggest that EGY1 metalloprotease is required for chloroplast development and, hence, a defective EGY1 gene has pleiotropic effects both on chloroplast development and on ethylene‐dependent gravitropism of light‐grown hypocotyls.
Early Cretaceous paleogeography of Korea and Southwest Japan inferred from occurrence of detrital chromian spinels
Authors: Hisada Ken‐ichiro , Takashima Shizuka , Arai Shoji , Lee Yong Il
Published: November 2008

The Sindong Group was deposited in the north–south trending half‐graben Nakdong Trough, southern Korean peninsula. The occurrence of detrital chromian spinels from the Jinju Formation of the Sindong Group in the Gyeongsang Basin means that the mafic to ultramafic rocks were exposed in its provenance. The chromian spinels from the Jinju Formation are characterized by extremely low TiO2 and Fe3+. Moreover, their range of Cr# is from 0.45 to 0.80 and makes a single trend with Mg#. The chemistry of chromian spinels implies that the source rocks for chromian spinels were peridotites or serpentinites, which originated in the mantle wedge. To more narrowly constrain their source rocks, the Ulsan and Andong serpentinites exposed in the Gyeongsang Basin were examined petrographically. Chromian spinels in the Andong serpentinite differ from those of the Jinju Formation and those in the Ulsan serpentinite partly resemble them. Furthermore, the Jinju chromian spinel suite is similar to the detrital chromian spinels from the Mesozoic sediments in the Circum‐Hida Tectonic zone, which includes the Nagato Tectonic zone in Southwest Japan and the Joetsu Belt in Northeast Japan. This suggests that the basement rocks, which were located along the main fault bounding the eastern edge of the Nakdong Trough, had exposures of peridotite or serpentinite. It is possible that the Nakdong Trough was directly adjacent to the Circum‐Hida Tectonic zone before the opening of the Sea of Japan (East Sea).
Influence of high‐dose methotrexate therapy on the primordial follicles of the mouse ovary
Authors: Gol Mert , Saygili Ugur , Koyuncuoglu Meral , Uslu Turhan
Published: November 2008

Objective:  High‐dose methotrexate (MTX) is one of the most prescribed agents in many malignant diseases affecting girls and young women of reproductive ages. This animal study directly measures the primordial follicle loss following exposure to high‐dose MTX.

Study Design:  Nine inbred Balb/c mice aged 7–8 weeks in the study group were administered 5 gr/m2 MTX as a single agent intraperitoneally, whereas nine mice in the control group received saline. Seven days later the mice were killed and total numbers of the primordial follicles remaining in both ovaries were counted.

Result:  In the high‐dose MTX group, the mean number of primordial follicles (mean ± standard deviation) was significantly different (202 ± 38) versus the control group (327 ± 81.7; P = 0.002).

Conclusions:  Our study shows that high‐dose MTX causes damage to the primordial follicles of the ovaries of mice. This result may be important because young women taking high‐dose MTX may suffer diminished reproductive performance and premature cessation of menses in the years following therapy.
Elevated level of serum retinol‐binding protein 4 in pregnancy‐induced hypertension
Authors: Inoue Seiji , Takamoto Norio , Akahori Yoichiro , Masumoto Akio , Nakatsukasa Hideki , Msuyama Hisashi , Hiramatsu Yuji
Published: November 2008

Aim:  Recent progress in adiposcience has revealed several important adipose‐tissue‐originated factors, so‐called adipokines. Retinol‐binding protein 4 (RBP4), a protein expressed and secreted by adipocytes, has been identified as a novel regulator of insulin resistance. Physiological insulin resistance occurs during the pregnancy of mammals to accommodate fetal growth, and it has been suggested that insulin resistance and hyperinsulinemia might also be associated with pregnancy‐induced hypertension (PIH). In order to shed light on the role of RBP4 during pregnancy, we attempted to assess RBP4 levels during pregnancy. Fetal growth could be affected by aberrant regulation of RBP4 levels in fetal circulation per se, so we examined the RBP4 levels in cord blood samples of growth restricted cases.

Methods:  Circulating RBP4 levels were examined in non‐pregnant and pregnant healthy women using Western blotting. Also, RBP4 levels in normal pregnancy and PIH were quantitated using Dot‐blot analysis. RBP4 levels in cord blood samples also were evaluated in selected cases.

Results:  RBP4 levels tended to decrease after early gestation with no obvious difference between mid‐ to late‐gestation. RBP4 levels were increased in pregnant women with PIH compared with normal pregnancies (P < 0.01). RBP4 levels were decreased in the cord blood of PIH pregnancies and light‐for‐dates infants without obvious causes for intrauterine growth restriction compared with normal pregnancies (P < 0.01).

Conclusions:  These results suggest that circulating RBP4 could be elevated in PIH, where maternal glucose metabolism is perturbed, and that RBP4 levels in cord blood might be closely associated with fetal growth.
Is the surgical approach beneficial to subfertile women with symptomatic extensive adenomyosis?
Authors: Wang Peng‐Hui , Fuh Jong‐Ling , Chao Hsiang‐Tai , Liu Wei‐Min , Cheng Ming‐Huei , Chao Kuan‐Chong
Published: November 2008

Aim:  Our aim was to assess the role of surgical intervention for symptom control and reproductive performance improvement in the management of subfertile women with symptomatic extensive uterine adenomyosis.

Methods:  Sixty‐five subfertile women with pathology‐proven extensive uterine adenomyosis, who were treated with conservative surgery or medical treatment with 6‐month gonadotrophin‐releasing hormone (GnRH) agonist or combination therapy, were retrospectively reviewed and their data analyzed. Twenty‐eight women received conservative surgery with/without GnRH agonist (group A), and 37 received 6‐month GnRH agonist therapy only (group B). Follow‐up evaluations, including subjective symptoms (a self‐reported 6‐point verbal numeric rating scale and an analgesic usage score for dysmenorrhea) and objective parameters (serum CA125 level, and uterine size), and clinical pregnancy and successful delivery rates were made semi‐annually over the ensuing 3 or more years.

Results:  The women in group A had higher serum CA125 levels, more infertile years, and a larger uterine size. Subjective symptom control and objective parameters were better in group A during the entire 36‐month follow up compared with those in group B. Cumulative 3‐year clinical pregnancy and successful delivery rates were significantly higher in group A, compared with those in group B (46.4% [13/28] versus 10.8% [4/37], P = 0.002, and 32.1% [9/28] versus 8.1% [3/37], P = 0.022, respectively).

Conclusion:  Conservative surgery or combination therapy provides more effective and longer durable symptom control in the management of symptomatic women with extensive uterine adenomyosis, compared with GnRH agonist alone. Reproductive performance was also better in patients treated with conservative surgery with/without GnRH agonist.
THE SPIRIT IN CREATION: A UNIFIED THEOLOGY OF GRACE AND CREATION CARE
Authors: Studebaker Steven M.
Published: November 2008

This essay identifies one of the deeper theological sources of the tendency toward environmental neglect in evangelical and Pentecostal theology and proposes a theological vision that facilitates a vision of creation care as a dimension of Christian formation. The first section identifies, describes, and evaluates the traditional distinction between common and special grace or the natural and the supernatural orders as a theological foundation for environmental neglect in Pentecostal theology. The second and third sections propose that a pneumatological vision of grace based on a fundamental trinitarianism provides Pentecostals and other Christians with a way to overcome these stark dualisms and to attain a more unified and comprehensive vision of God's grace that is more conducive to creation care. The fourth section presents a case for seeing creation care as a pneumatological and proleptic participation in the eschaton and, as such, as a dimension of Christian formation and sanctification.