bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth of high quality N-polar AlN(0001¯) on Si(111) by plasma assisted molecular beam epitaxy
Authors: Dasgupta Sansaptak , Wu F. , Speck J. S. , Mishra U. K.
Published: April 2009

High quality N-polar AlN epilayers were grown and characterized on Si(111) substrates by plasma assisted molecular beam epitaxy as a first step toward growth of N-polar nitrides on Si(111). Polarity inversion to N-face by an optimized predeposition of Al adatoms on the reconstructed 7×7 Si(111) surface was investigated. Al adatoms can saturate the dangling bonds of Si atoms, resulting in growth of AlN in (0001¯) direction on subsequent exposure to N2 plasma. N-polarity was confirmed by observing strong 3×3 and 6×6 reflection high-energy electron diffraction reconstructions, convergent beam electron diffraction imaging and KOH etching studies. The structural properties were investigated by x-ray diffraction measurements, cross section and plan-view TEM studies.
Coulomb blockade effect and negative differential resistance in the electronic transport of bacteriorhodopsin
Authors: Kim Jong-Yeob , Lee Sunbae , Yoo Kyung-Hwa , Jang Du-Jeon
Published: April 2009

A functional protein of bacteriorhodopsin has been employed for an approach to develop molecular single-electron transistors. A purple-membrane nanofragment shows a characteristic, cyclic, and reproducible I-V curve having negative differential resistance and an on-off peak-to-valley ratio of 660. The conductance increases exponentially with temperature increase with an activation energy of 47 meV, comparable to the charging energy of a bacteriorhodopsin molecule. This with observed I-V scaling relationship indicates that the Coulomb blockade is the primary conductance-limiting feature and that charges are carried by arrayed Coulomb islands of bacteriorhodopsin.
Athermal all-optical femtosecond magnetization reversal in GdFeCo
Authors: Hohlfeld J. , Stanciu C. D. , Rebei A.
Published: April 2009

Magnetization reversal in GdFeCo by circularly polarized light is shown to occur at the femtosecond time scale. In contrast to the well-known laser-assisted magnetization reversal based on the laser heating, we here demonstrate that this femtosecond all-optical magnetization reversal is more efficient at lower temperatures. Both of these findings make all-optical recording on rare-earth transition metal alloys a promising technique for stable magnetic storage with high data rates.
Ordered amorphous silicon nanoisland arrays and reflection spectral dependence on nanoisland geometrical parameters
Authors: Liu L. Z. , Huang G. S. , Wang L. L. , Li T. H. , Wu X. L.
Published: April 2009

We report an anodic porous alumina mask technique for fabricating orderly hemispherical silicon nanoisland arrays with island diameters of 30–120 nm. Reflection spectral measurements show that the phase transition of incident light can periodically be transferred with changes in geometrical parameters of the ordered arrays. Thus the redshift of the reflection peak with decreasing both sizes of the nanoislands and incident angle of light wave can be explained well on the basis of a modified rigorous vector coupled-wave theory. The simple fabrication technique and reflection spectral redshift of the ordered arrays have potential applications in optical devices and solar cells.
Low effective barrier height of GaOx tunnel barrier in metal/semiconductor hybrid junctions
Authors: Le Breton J. C. , Saito H. , Yuasa S. , Ando K.
Published: April 2009

We measured the resistance-area products (RAs) in Fe/GaOx/n-(Al)GaAs junctions with respect to the GaOx thickness d. A good linear relation was observed in the log(RA)-d plot, indicating a high-quality tunnel junction. We found that the effective barrier height ϕ in the Fe/GaOx/AlGaAs was very low at 0.10 eV at room temperature. Such a low ϕ with excellent tunability in RA strongly suggests that GaOx is a promising tunnel-barrier material for GaAs-based spin-utilized devices.
Continuous wave second-harmonic generation using domain-disordered quasi-phase matching waveguides
Authors: Wagner Sean J. , Holmes Barry M. , Younis Usman , Helmy Amr S. , Aitchison J. Stewart , Hutchings David C.
Published: April 2009

Second-harmonic generation in domain-disordered quasi-phase-matched GaAs/AlGaAs superlattice-core waveguides was demonstrated using a continuous wave fundamental source. Output second-harmonic powers of up to 1.6 μW were measured when on a Fabry-Pérot resonance peak. Temperature-related bistable behavior was observed in both the fundamental and second-harmonic output when tuning either the input power or input wavelength.
Coercivity of nanoporous Ni produced by dealloying
Authors: Hakamada Masataka , Takahashi Masaki , Furukawa Toshiyuki , Mabuchi Mamoru
Published: April 2009

Nanoporous Ni specimens with the ligament lengths of 10–210 nm were produced by the dealloying of Ni0.25Mn0.75 alloy and annealing at 473–873 K. The coercivity (Hc) increased with increasing ligament length (L) up to 50 nm, and decreased with increasing L above 50 nm. At L<50 nm, the size dependence of Hc for nanoporous Ni is lower than that for nanocrystalline Ni. The low size dependence of Hc is discussed on basis of a random anisotropy model.
Parallel imaging/manipulation force microscopy
Authors: Xie H. , Haliyo D. S. , Régnier S.
Published: April 2009

Conventional atomic force microscope nanomanipulation is inefficient because of the serial imaging/manipulation operation. We present here a parallel imaging/manipulation force microscope (PIMM) to improve manipulation efficiency. The PIMM is equipped with two individually actuated cantilevers with protrudent tips. One cantilever acts as an imaging sensor by scanning nano-objects and tip of the other cantilever that is used as a manipulating tool. Two manipulation schemes were introduced to fulfill parallel imaging/manipulation tasks with normal and high-speed image scan, respectively. Performance of the PIMM was validated by the parallel imaging/manipulation of nanoparticles to form a nanopattern with a commonly used pushing operation.
Ab initio study of lithium and sodium iron fluorophosphate cathodes for rechargeable batteries
Authors: Ramzan M. , Lebègue S. , Ahuja R.
Published: April 2009

The cathode materials Li2FePO4F and Na2FePO4F are studied by means of ab initio calculations. The generalized gradient approximation (GGA) and GGA+U are used to describe the crystal structures, and the electronic and magnetic properties of Li2FePO4F, Na2FePO4F, LiFePO4F, and NaFePO4F. Since only the lattice parameters are known for Li2FePO4F, our calculations predict the corresponding atomic positions, and reveal that the iron atom state (FeIII or FeII) is changed during the reaction, which is of importance to understand the reactions taking place in rechargeable batteries. Finally, our calculated intercalation voltage with the GGA+U approximation is in good agreement with experimental value.
Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5
Authors: Zhou Karen , Kuo Wei Hung William , Fillingham Jeffrey , Greenblatt Jack F.
Published: April 2009

Elongation by RNA polymerase II (RNAPII) is a finely regulated process in which many elongation factors contribute to gene regulation. Among these factors are the polymerase-associated factor (PAF) complex, which associates with RNAPII, and several cyclin-dependent kinases, including positive transcription elongation factor b (P-TEFb) in humans and BUR kinase (Bur1–Bur2) and C-terminal domain (CTD) kinase 1 (CTDK1) in
Saccharomyces cerevisiae
. An important target of P-TEFb and CTDK1, but not BUR kinase, is the CTD of the Rpb1 subunit of RNAPII. Although the essential BUR kinase phosphorylates Rad6, which is required for histone H2B ubiquitination on K123, Rad6 is not essential, leaving a critical substrate(s) of BUR kinase unidentified. Here we show that BUR kinase is important for the phosphorylation in vivo of Spt5, a subunit of the essential yeast RNAPII elongation factor Spt4/Spt5, whose human orthologue is DRB sensitivity-inducing factor. BUR kinase can also phosphorylate the C-terminal region (CTR) of Spt5 in vitro. Like BUR kinase, the Spt5 CTR is important for promoting elongation by RNAPII and recruiting the PAF complex to transcribed regions. Also like BUR kinase and the PAF complex, the Spt5 CTR is important for histone H2B K123 monoubiquitination and histone H3 K4 and K36 trimethylation during transcription elongation. Our results suggest that the Spt5 CTR, which contains 15 repeats of a hexapeptide whose consensus sequence is S[T/A]WGG[A/Q], is a substrate of BUR kinase and a platform for the association of proteins that promote both transcription elongation and histone modification in transcribed regions.
Squeezing out the entropy of fermions in optical lattices
Authors: Ho Tin-Lun , Zhou Qi
Published: April 2009

At present, there is considerable interest in using atomic fermions in optical lattices to emulate the mathematical models that have been used to study strongly correlated electronic systems. Some of these models, such as the 2-dimensional fermion Hubbard model, are notoriously difficult to solve, and their key properties remain controversial despite decades of studies. It is hoped that the emulation experiments will shed light on some of these long-standing problems. A successful emulation, however, requires reaching temperatures as low as 10
−12
K and beyond, with entropy per particle far lower than what can be achieved today. Achieving such low-entropy states is an essential step and a grand challenge of the whole emulation enterprise. In this article, we point out a method to literally squeeze the entropy out from a Fermi gas into a surrounding Bose–Einstein condensed gas, which acts as a heat reservoir. This method allows one to reduce the entropy per particle of a lattice Fermi gas to a few percent of the lowest value obtainable today.
Temporal lags and overlap in the diversification of weevils and flowering plants
Authors: McKenna Duane D. , Sequeira Andrea S. , Marvaldi Adriana E. , Farrell Brian D.
Published: April 2009

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on ≈8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning ≈166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca.112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.
Ancient Egyptian herbal wines
Authors: McGovern Patrick E. , Mirzoian Armen , Hall Gretchen R.
Published: April 2009

Chemical analyses of ancient organics absorbed into pottery jars from the beginning of advanced ancient Egyptian culture,
ca
. 3150 B.C., and continuing for millennia have revealed that a range of natural products—specifically, herbs and tree resins—were dispensed by grape wine. These findings provide chemical evidence for ancient Egyptian organic medicinal remedies, previously only ambiguously documented in medical papyri dating back to
ca
. 1850 B.C. They illustrate how humans around the world, probably for millions of years, have exploited their natural environments for effective plant remedies, whose active compounds have recently begun to be isolated by modern analytical techniques.
A right-sided pathway involving
FGF8
/
Snai1
controls asymmetric development of the proepicardium in the chick embryo
Authors: Schlueter Jan , Brand Thomas
Published: April 2009

The proepicardium (PE) is a transient structure that forms at the venous pole of the embryonic vertebrate heart. This cardiac progenitor cell population gives rise to the epicardium, coronary vasculature, and fibroblasts. In the chicken embryo, the PE displays left-right (L-R) asymmetry and develops only on the right side, while on the left only a vestigial PE is formed, which subsequently gets lost by apoptosis. In this study, we analyzed how the L-R asymmetry pathway affects PE formation. Experimental manipulation of left-side determinants such as Shh, Nodal, and Cfc as well as forced expression of Pitx2 had no effect on the sidedness of PE development. In contrast, inhibition of early-acting regulators of L-R axis formation such as H
+
/K
+
-ATPase or primitive streak apoptosis affected the sidedness of PE development. Experimental interference with the right-side determinants Fgf8 or Snai1 prevented PE formation, whereas ectopic left-sided expression of Fgf8 or Snai1 resulted in bilateral PE development. These data provide novel insight into the molecular control of asymmetric morphogenesis suggesting that also the right side harbors an instructive signaling pathway that is involved in the control of PE development. This pathway might be of general relevance for setting up L-R asymmetries at the venous pole of the heart.
Averting epidemics of extensively drug-resistant tuberculosis
Authors: Basu Sanjay , Friedland Gerald H. , Medlock Jan , Andrews Jason R. , Shah N. Sarita , Gandhi Neel R. , Moll Anthony , Moodley Prashini , Sturm A. Willem , Galvani Alison P.
Published: April 2009

Extensively drug-resistant tuberculosis (XDR TB) has been detected in most provinces of South Africa, particularly in the KwaZulu-Natal province where several hundred cases have been reported since 2004. We analyzed the transmission dynamics of XDR TB in the region using mathematical models, and observed that nosocomial transmission clusters of XDR TB may emerge into community-based epidemics under the public health conditions of many South African communities. The effective reproductive number of XDR TB in KwaZulu-Natal may be around 2. Intensified community-based case finding and therapy appears critical to curtailing transmission. In the setting of delayed disease presentation and high system demand, improved diagnostic approaches may need to be employed in community-based programs rather than exclusively at tertiary hospitals. Using branching process mathematics, we observed that early, community-based drug-susceptibility testing and effective XDR therapy could help curtail ongoing transmission and reduce the probability of XDR TB epidemics in neighboring territories.
Functional morphology of the ankle and the likelihood of climbing in early hominins
Authors: DeSilva Jeremy M.
Published: April 2009

Whether early hominins were adept tree climbers is unclear. Although some researchers have argued that bipedality maladapts the hominin skeleton for climbing, others have argued that early hominin fossils display an amalgamation of features consistent with both locomotor strategies. Although chimpanzees have featured prominently in these arguments, there are no published data on the kinematics of climbing in wild chimpanzees. Without these biomechanical data describing how chimpanzees actually climb trees, identifying correlates of climbing in modern ape skeletons is difficult, thereby limiting accurate interpretations of the hominin fossil record. Here, the first kinematic data on vertical climbing in wild chimpanzees are presented. These data are used to identify skeletal correlates of climbing in the ankle joint of the African apes to more accurately interpret hominin distal tibiae and tali. This study finds that chimpanzees engage in an extraordinary range of foot dorsiflexion and inversion during vertical climbing bouts. Two skeletal correlates of modern ape-like vertical climbing are identified in the ankle joint and related to positions of dorsiflexion and foot inversion. A study of the 14 distal tibiae and 15 tali identified and published as hominins from 4.12 to 1.53 million years ago finds that the ankles of early hominins were poorly adapted for modern ape-like vertical climbing bouts. This study concludes that if hominins included tree climbing as part of their locomotor repertoire, then they were performing this activity in a manner decidedly unlike modern chimpanzees.
Prolonged duration local anesthesia with minimal toxicity
Authors: Epstein-Barash Hila , Shichor Iris , Kwon Albert H. , Hall Sherwood , Lawlor Michael W. , Langer Robert , Kohane Daniel S.
Published: April 2009

Injectable local anesthetics that would last for many days could have a marked impact on periprocedural care and pain management. Formulations have often been limited in duration of action, or by systemic toxicity, local tissue toxicity from local anesthetics, and inflammation. To address those issues, we developed liposomal formulations of saxitoxin (STX), a compound with ultrapotent local anesthetic properties but little or no cytotoxicity. In vitro, the release of bupivacaine and STX from liposomes depended on the lipid composition and on whether dexamethasone was incorporated. In cell culture, bupivacaine, but not STX, was myotoxic (to C2C12 cells) and neurotoxic (to PC12 cells) in a concentration- and time-dependent manner. Liposomal formulations containing combinations of the above compounds produced sciatic nerve blockade lasting up to 7.5 days (with STX + dexamethasone liposomes) in male Sprague–Dawley rats. Systemic toxicity only occurred where high loadings of dexamethasone increased the release of liposomal STX. Mild myotoxicity was only seen in formulations containing bupivacaine. There was no nerve injury on Epon-embedded sections, and these liposomes did not up-regulate the expression of 4 genes associated with nerve injury in the dorsal root ganglia. These results suggest that controlled release of STX and similar compounds can provide very prolonged nerve blocks with minimal systemic and local toxicity.
Remarkable resilience of teeth
Authors: Chai Herzl , Lee James J.-W. , Constantino Paul J. , Lucas Peter W. , Lawn Brian R.
Published: April 2009

Tooth enamel is inherently weak, with fracture toughness comparable with glass, yet it is remarkably resilient, surviving millions of functional contacts over a lifetime. We propose a microstructural mechanism of damage resistance, based on observations from ex situ loading of human and sea otter molars (teeth with strikingly similar structural features). Section views of the enamel implicate tufts, hypomineralized crack-like defects at the enamel–dentin junction, as primary fracture sources. We report a stabilization in the evolution of these defects, by “stress shielding” from neighbors, by inhibition of ensuing crack extension from prism interweaving (decussation), and by self-healing. These factors, coupled with the capacity of the tooth configuration to limit the generation of tensile stresses in largely compressive biting, explain how teeth may absorb considerable damage over time without catastrophic failure, an outcome with strong implications concerning the adaptation of animal species to diet.
FAK alters invadopodia and focal adhesion composition and dynamics to regulate breast cancer invasion
Authors: Chan Keefe T. , Cortesio Christa L. , Huttenlocher Anna
Published: April 2009

Focal adhesion kinase (FAK) is important for breast cancer progression and invasion and is necessary for the dynamic turnover of focal adhesions. However, it has not been determined whether FAK also regulates the dynamics of invasive adhesions formed in cancer cells known as invadopodia. In this study, we report that endogenous FAK functions upstream of cellular Src (c-Src) as a negative regulator of invadopodia formation and dynamics in breast cancer cells. We show that depletion of FAK induces the formation of active invadopodia but impairs invasive cell migration. FAK-deficient MTLn3 breast cancer cells display enhanced assembly and dynamics of invadopodia that are rescued by expression of wild-type FAK but not by FAK that cannot be phosphorylated at tyrosine 397. Moreover, our findings demonstrate that FAK depletion switches phosphotyrosine-containing proteins from focal adhesions to invadopodia through the temporal and spatial regulation of c-Src activity. Collectively, our findings provide novel insight into the interplay between FAK and Src to promote invasion.
A c-Myc–SIRT1 feedback loop regulates cell growth and transformation
Authors: Yuan Jian , Minter-Dykhouse Katherine , Lou Zhenkun
Published: April 2009

The protein deacetylase SIRT1 has been implicated in a variety of cellular functions, including development, cellular stress responses, and metabolism. Increasing evidence suggests that similar to its counterpart, Sir2, in yeast, Caenorhabditis elegans, and Drosophila melanogaster, SIRT1 may function to regulate life span in mammals. However, SIRT1's role in cancer is unclear. During our investigation of SIRT1, we found that c-Myc binds to the SIRT1 promoter and induces SIRT1 expression. However, SIRT1 interacts with and deacetylates c-Myc, resulting in decreased c-Myc stability. As a consequence, c-Myc's transformational capability is compromised in the presence of SIRT1. Overall, our experiments identify a c-Myc–SIRT1 feedback loop in the regulation of c-Myc activity and cellular transformation, supporting/suggesting a role of SIRT1 in tumor suppression.
Early endosomes and endosomal coatomer are required for autophagy
Authors: Razi Minoo , Chan Edmond Y.W. , Tooze Sharon A.
Published: April 2009

Autophagy, an intracellular degradative pathway, maintains cell homeostasis under normal and stress conditions. Nascent double-membrane autophagosomes sequester and enclose cytosolic components and organelles, and subsequently fuse with the endosomal pathway allowing content degradation. Autophagy requires fusion of autophagosomes with late endosomes, but it is not known if fusion with early endosomes is essential. We show that fusion of AVs with functional early endosomes is required for autophagy. Inhibition of early endosome function by loss of COPI subunits (β′, β, or α) results in accumulation of autophagosomes, but not an increased autophagic flux. COPI is required for ER-Golgi transport and early endosome maturation. Although loss of COPI results in the fragmentation of the Golgi, this does not induce the formation of autophagosomes. Loss of COPI causes defects in early endosome function, as both transferrin recycling and EGF internalization and degradation are impaired, and this loss of function causes an inhibition of autophagy, an accumulation of p62/SQSTM-1, and ubiquitinated proteins in autophagosomes.
Caspase-2 activation in the absence of PIDDosome formation
Authors: Manzl Claudia , Krumschnabel Gerhard , Bock Florian , Sohm Benedicte , Labi Verena , Baumgartner Florian , Logette Emmanuelle , Tschopp Jürg , Villunger Andreas
Published: April 2009

PIDD (p53-induced protein with a death domain [DD]), together with the bipartite adapter protein RAIDD (receptor-interacting protein-associated ICH-1/CED-3 homologous protein with a DD), is implicated in the activation of pro–caspase-2 in a high molecular weight complex called the PIDDosome during apoptosis induction after DNA damage. To investigate the role of PIDD in cell death initiation, we generated PIDD-deficient mice. Processing of caspase-2 is readily detected in the absence of PIDDosome formation in primary lymphocytes. Although caspase-2 processing is delayed in simian virus 40–immortalized pidd−/− mouse embryonic fibroblasts, it still depends on loss of mitochondrial integrity and effector caspase activation. Consistently, apoptosis occurs normally in all cell types analyzed, suggesting alternative biological roles for caspase-2 after DNA damage. Because loss of either PIDD or its adapter molecule RAIDD did not affect subcellular localization, nuclear translocation, or caspase-2 activation in high molecular weight complexes, we suggest that at least one alternative PIDDosome-independent mechanism of caspase-2 activation exists in mammals in response to DNA damage.
Mast cells mediate neutrophil recruitment and vascular leakage through the NLRP3 inflammasome in histamine-independent urticaria
Authors: Nakamura Yuumi , Kambe Naotomo , Saito Megumu , Nishikomori Ryuta , Kim Yun-Gi , Murakami Makoto , Núñez Gabriel , Matsue Hiroyuki
Published: April 2009

Urticarial rash observed in cryopyrin-associated periodic syndrome (CAPS) caused by nucleotide-binding oligomerization domain–leucine-rich repeats containing pyrin domain 3 (NLRP3) mutations is effectively suppressed by anti–interleukin (IL)-1 treatment, suggesting a pathophysiological role of IL-1β in the skin. However, the cellular mechanisms regulating IL-1β production in the skin of CAPS patients remain unclear. We identified mast cells (MCs) as the main cell population responsible for IL-1β production in the skin of CAPS patients. Unlike normal MCs that required stimulation with proinflammatory stimuli for IL-1β production, resident MCs from CAPS patients constitutively produced IL-1β. Primary MCs expressed inflammasome components and secreted IL-1β via NLRP3 and apoptosis-associated speck-like protein containing a caspase recruitment domain when stimulated with microbial stimuli known to activate caspase-1. Furthermore, MCs expressing disease-associated but not wild-type NLRP3 secreted IL-1β and induced neutrophil migration and vascular leakage, the histological hallmarks of urticarial rash, when transplanted into mouse skin. Our findings implicate MCs as IL-1β producers in the skin and mediators of histamine-independent urticaria through the NLRP3 inflammasome.
Channel-like slippage modes in the human anion/proton exchanger ClC-4
Authors: Alekov Alexi K. , Fahlke Christoph
Published: April 2009

The ClC family encompasses two classes of proteins with distinct transport functions: anion channels and transporters. ClC-type transporters usually mediate secondary active anion–proton exchange. However, under certain conditions they assume slippage mode behavior in which proton and anion transport are uncoupled, resulting in passive anion fluxes without associated proton movements. Here, we use patch clamp and intracellular pH recordings on transfected mammalian cells to characterize exchanger and slippage modes of human ClC-4, a member of the ClC transporter branch. We found that the two transport modes differ in transport mechanisms and transport rates. Nonstationary noise analysis revealed a unitary transport rate of 5 × 105 s−1 at +150 mV for the slippage mode, indicating that ClC-4 functions as channel in this mode. In the exchanger mode, unitary transport rates were 10-fold lower. Both ClC-4 transport modes exhibit voltage-dependent gating, indicating that there are active and non-active states for the exchanger as well as for the slippage mode. ClC-4 can assume both transport modes under all tested conditions, with exchanger/channel ratios determined by the external anion. We propose that binding of transported anions to non-active states causes transition from slippage into exchanger mode. Binding and unbinding of anions is very rapid, and slower transitions of liganded and non-liganded states into active conformations result in a stable distribution between the two transport modes. The proposed mechanism results in anion-dependent conversion of ClC-type exchanger into an anion channel with typical attributes of ClC anion channels.
The zig‐zag‐zig in oomycete–plant interactions
Authors: HEIN INGO , GILROY ELEANOR M. , ARMSTRONG MILES R. , BIRCH PAUL R. J.
Published: April 2009

In addition to a range of preformed barriers, plants defend themselves against microbial invasion by detecting conserved, secreted molecules, called pathogen‐associated molecular patterns (PAMPs). PAMP‐triggered immunity (PTI) is the first inducible layer of plant defence that microbial pathogens must navigate by the delivery of effector proteins that act to suppress or otherwise manipulate key components of resistance. Effectors may themselves be targeted by a further layer of defence, effector‐triggered immunity (ETI), as their presence inside or outside host cells may be detected by resistance proteins. This ‘zig‐zag‐zig’ of tightly co‐evolving molecular interactions determines the outcome of attempted infection. In this article, we consider the complex molecular interplay between plants and plant pathogenic oomycetes, drawing on recent literature to illustrate what is known about oomycete PAMPs and elicitors of defence responses, the effectors they utilize to suppress PTI, and the phenomenal molecular ‘battle’ between effector and resistance (R) genes that dictates the establishment or evasion of ETI.
Present‐day stresses in Brunei, NW Borneo: superposition of deltaic and active margin tectonics
Authors: King R. C. , Hillis R. R. , Tingay M. R. P. , Damit A.‐R.
Published: April 2009

The Baram Delta System, Brunei, NW Borneo, is a Tertiary delta system located on an active continental margin. Delta top regions in many Tertiary delta systems (e.g. Niger Delta) are thought to exhibit a normal‐fault stress regime and margin‐parallel maximum horizontal stress orientations. However, unlike in passive margin Tertiary delta systems, two present‐day stress provinces have been previously identified across the Baram Delta System: an inner shelf inverted province with a margin‐normal (NW–SE) maximum horizontal stress orientation and an outer shelf extension province with a margin‐parallel (NE–SW) maximum horizontal stress orientation. Before this study, there were few data constraining the inverted province other than in the vicinity of the Champion Fields. New data from 12 petroleum wells in the western inner shelf and onshore west Brunei presented herein confirm the margin‐normal maximum horizontal stress orientations of the inverted province. A total of 117 borehole breakouts, all documented in shale units, and one drilling‐induced tensile fracture (in a sandstone interval) reveal a mean maximum horizontal stress orientation of 117 with a standard deviation of 19°. This orientation is consistent with contemporary margin‐normal maximum horizontal stress orientations of the inverted province described previously in the vicinity of the Champion Fields that have been linked to basement tectonics of the Crocker–Rajang accretionary complex and associated active margin. However, stress magnitudes calculated using data from these 12 petroleum wells indicate a borderline strike–slip fault to normal fault stress regime for the present day; combined with the absence of seismicity, this suggests that the studied part of the NW Borneo continental margin is currently tectonically quiescent.
T cells and eosinophils in bronchial smooth muscle cell death in asthma
Authors: Solarewicz‐Madejek K. , Basinski T. M. , Crameri R. , Akdis M. , Akkaya A. , Blaser K. , Rabe K. F. , Akdis C. A. , Jutel M.
Published: April 2009

Background
Bronchial smooth muscle cells (SMC) proliferate, express adhesion molecules, secrete cytokines and thus efficiently contribute to the pathogenesis of asthma.

Objective
The aim of the study was to investigate whether, and by which mechanism, T cells and eosinophils can cause death of airway SMC.

Methods
The T cell‐ and eosinophil‐induced cell death was analysed in primary human bronchial SMC cultures as well as in bronchial biopsy specimens from non‐asthmatic and asthmatic individuals.

Results
Bronchial SMC death showed characteristic morphological features of apoptosis in 3–6 days cultures with inflammatory cytokines (IFN‐γ, TNF‐α), soluble death ligands [sFasL, TNF‐related apoptosis‐inducing ligand (TRAIL)] and activated T‐helper type 1 (Th1) and Th2 cell supernatants. The recombinant eosinophil cationic protein induced SMC necrosis within 1 h. Resting SMC expressed the death receptors TNFR1, TNFR2, Fas, TRAILR1, TRAILR2 and membrane FasL as a death‐inducing ligand. IFN‐γ and TNF‐α up‐regulated TNFR1, TNFR2, Fas and membrane FasL on SMC. TNF‐α up‐regulated TRAILR1 and TRAILR2; sFasL up‐regulated TNFR2. The intracellular caspase‐3 activation in SMC was significantly increased by IFN‐γ, sFasL, TRAIL, Th1 and Th2 cell supernatants. Increased expression of TRAIL in asthmatics, but not in non‐asthmatic individuals was demonstrated in situ. The apoptosis receptors TRAILR1 and TRAILR2 were expressed in SMC and epithelial cells both in healthy and asthmatic biopsies. Prominent apoptosis of SMC was observed in fatal asthma, but not intermittent asthma biopses.

Conclusion
The demonstration of bronchial SMC death both by apoptosis and necrosis indicates the essential role of T cells and eosinophils in the bronchial tissue injury particularly in the severe asthma.
Age at puberty in male African striped mice: the impact of food, population density and the presence of the father
Authors: Schradin Carsten , Schneider Carola , Yuen Chi Hang
Published: April 2009

1. The time at which animals enter puberty and become sexually mature is a significant life‐history trait, influencing lifetime reproductive success. Great variation exists both between and within species.

2. The proximate mechanisms regulating the time at which a male enters puberty are not well‐understood. Environmental cues are predicted to provide the relevant information on resource availability and opportunities for reproduction. When these are good the onset of puberty begins whereas at other times investment in survival becomes more important.

3. Male African striped mice (Rhabdomys pumilio) demonstrate large variation in the age at which they enter puberty, with grassland populations starting at 4 weeks old and semi‐desert populations at over 10 weeks old.

4. We predicted that differences in the availability of food, social organization and population density could explain these differences.

5. Using data on 170 individual males from 4 years of field studies in a semi‐desert population, we found that males became scrotal at a younger age when no breeding male was present in their group and when food was abundant, while population density had no effect.

6. In laboratory experiments we demonstrated that males fed with poor protein food, that regularly encounter larger unfamiliar males (mimicking high population density), and that live in family groups with their father present, become scrotal at a significantly later age, independent of their growth rate.

7. Males housed in family groups have lower testosterone but higher corticosterone levels than singly housed males, indicating they are sexually suppressed. When they become scrotal in their family group, their testes are only half as large as those of their singly housed brothers, and they contained significantly less sperm.

8. We conclude that male striped mice have a flexible response to the onset of puberty, and that the onset of sexual maturity is dependent on several environmental cues. Our results indicate that there is no threshold body mass, which, when reached, would automatically trigger puberty in male striped mice.

9. Male helpers in some species are reproductively suppressed, but ours is the first study that demonstrated the importance of different ecological factors in the timing of puberty in male helpers in a facultative cooperatively breeding species.
Influence of solvent and temperature on extraction of phenolic compounds from grape seed, antioxidant activity and colour of extract
Authors: Bucić‐Kojić Ana , Planinić Mirela , Tomas Srećko , Jakobek Lidija , Šeruga Marijan
Published: April 2009

This study was aimed to investigate the influence of solvent (water and ethanol in concentration: 50%, 70% and 96%) and extraction temperature (25–80) °C on polyphenols extraction of grape seed (Vitis viniferaL. cv. “Frankovka”) cultivated in Eastern Croatia. The best results were reached using 50% ethanol at 80 °C. The most abundant individual polyphenolic compound was catechin which makes the average of 45.11% of the total phenolic content followed by epicatechin (34.45%), procyanidin B2(12.90%), gallic acid (5.34%), gallocatechin (1.58%), epicatechin gallate (1.01%). The antioxidant activity of extracts was determined by DPPH‐method and it was highly dependent on extraction solvent and temperature. The total extractable proanthocyanidins content of extract had the highest positive correlation (r = 0.994) with antioxidant activity, which indicated that these compounds might be the most important antioxidant in examined grape seed extracts. Relationship between phenolic content and colour of extracts was observed.
Natural preservative ingredient from marine alga Ulva lactuca L.
Authors: Abd El‐Baky Hanaa H. , El‐Baz Farouk K. , El‐Baroty Gamal S.
Published: April 2009

The contents of total chlorophyll (T‐Chl), carotenoids and phenolics compounds were quantified in the biomasses of Ulva lactuca grown either in normal or artificial sea water under indoor conditions. The antioxidant and antibacterial activities of U. lactuca crude organic extracts (Ulva‐COEs) were determined. Thirty‐four compounds in Ulva‐COEs were characterised by thin layer chromatography and high‐performance liquid chromatography. The major compounds were chlorophyll a (Chl a) (15.60–30.90%) and b (Chl b) (12.20–14.89%), 9‐cis β‐carotene (13.12–14.47%), α‐carotene (11.44–11.47%) and all‐trans β‐carotene (6.16–29.70%, of total carotenoids).The Ulva‐COEs exhibited remarkable antioxidant activity, with an IC50 (concentration which causes a 50% of DPPH radical scavenging activity) values ranged from 16.5 and 18.7 μg mL−1, which could be compared with the synthetic antioxidants: α‐tocopherol (14.4 μg mL−1), butylated hydroxyanisol (13.1 μg mL−1) and butylated hydroxyltoluene (13.1 μg mL−1). Also, Ulva‐COEs exhibited great potential antibacterial activities against six bacterial strains, with minimal inhibitory concentration values ranged from 0.40 to 0.35 mg mL−1.
Gear‐based fisheries management as a potential adaptive response to climate change and coral mortality
Authors: Cinner Joshua E. , McClanahan Tim R. , Graham Nicholas A. J. , Pratchett Morgan S. , Wilson Shaun K. , Raina Jean‐Baptiste
Published: April 2009

Climate change is emerging as one of the greatest threats to coral reef ecosystems. Climate‐induced warming events trigger coral bleaching and mortality, which can indirectly affect coral reef fishes. Managing fisheries across coral mortality events is expected to influence the persistence of species and reef recovery potential. The most common management recommendation has been to prohibit fishing using fisheries closures, but this response often has limited support from resource users.

Here, we explore an alternative of managing fishing gear commonly used in artisanal coral reef fisheries. We examined fisheries landing data from 15 sites in Papua New Guinea and Kenya to explore whether or how specific gears select for: (i) species that depend on coral reefs for feeding or habitat and are likely to be susceptible to the loss of coral, and (ii) different functional groups of fishes.

Only 6% of the fishes targeted by fishers were susceptible to the immediate effects of coral mortality; however, loss of habitat structure following coral mortality is expected to affect 56% of targeted species.

Importantly, 25% of target species had feeding characteristics (i.e. reef scrapers/excavators and grazers) that contribute to the recovery of coral reef ecosystems, and gears differed considerably in catches of these species.

Spear guns and traps target a high proportion of species likely to be affected by bleaching and key for the recovery of corals. These gears are strong candidates for management restrictions in reefs with high coral mortality. In contrast, line fishing catches the lowest proportion of susceptible and recovery‐enabling species and is preferential for increasing recovery rates on coral reefs.

Synthesis and applications. Fisheries managers will require a range of tools to meet the novel challenges posed by climate change. This study presents a way to help reduce the negative impacts of climate change and potentially increase resilience of marine ecosystems by managing fishing gear. Specific gears used by artisanal fishers differentially target fish functional groups. In the coral reefs that we studied, traps and spear guns targeted a high proportion of species highly susceptible to coral mortality and critical to coral reef resilience through their top‐down control. Given that full fisheries closures are not always practical, selectively banning or restricting fishing gears is a potentially powerful tool for reducing the detrimental ecosystem effects of climate change disturbances.
Heterologous hybridization to a complementary DNA microarray reveals the effect of thermal acclimation in the endothermic bluefin tuna (Thunnus orientalis)
Authors: CASTILHO PEDRO C. , BUCKLEY BRADLEY A. , SOMERO GEORGE , BLOCK BARBARA A.
Published: April 2009

The temperature stress that pelagic fishes experience can induce physiological and behavioural changes that leave a signature in gene expression profiles. We used a functional genomics approach to identify genes that were up‐ or down‐regulated following thermal stress in the Pacific bluefin tuna. Following the acclimation period, 113, 81 and 196 genes were found to be differentially expressed between the control (20 °C) and cold (15°) treatment groups, in ventricle, red muscle and white muscle, respectively. The genes whose expression levels were responsive to thermal acclimation varied according to muscle fibre type, perhaps reflecting the tissue‐specific degrees of endothermy characteristic of this species.
Reticulate evolution on a mosaic of soils: diversification of the New Caledonian endemic genus Codia (Cunoniaceae)
Authors: PILLON YOHAN , MUNZINGER JÉRÔME , AMIR HAMID , HOPKINS HELEN C. F. , CHASE MARK W.
Published: April 2009

We reconstructed the evolutionary history of Codia, a plant genus endemic to the New Caledonia biodiversity hotspot in the southwest Pacific, using three single‐copy nuclear genes. It seems likely that more than half of Codia species have a hybrid origin, but in the absence of cytological information, it is not known whether polyploids occur. Adaptation to ultramafic soils is possibly a plesiomorphic character for the entire genus. We found that species of hybrid origin can have some morphological characters absent in putative parental species, that is, they exhibit transgressive phenotypes. There is evidence of considerable range alteration post‐origin in several species because some likely parental species of hybrid taxa no longer co‐occur and are confined to putative rainforest refugia; in some cases, hybrid species do not now co‐occur with either of their parental species. These results have implications for the design of conservation strategies, for example, prioritization of parental species for ex‐situ conservation and preservation of the contact zones between soil types where hybridization is more likely to occur (i.e. conserving the possibility for the process to continue rather than trying to conserve taxa).
From alpha to beta: identification of amino acids required for the N‐acetyllactosamine‐specific lectin‐like activity of bundlin
Authors: Humphries Romney M. , Donnenberg Michael S. , Strecker Jonathan , Kitova Elena , Klassen John S. , Cui Lina , Griener Thomas P. , Mulvey George L. , Armstrong Glen D.
Published: April 2009

Bundle‐forming pili (BFP) promote the adherence of typical enteropathogenic Escherichia coli (EPEC) to human intestinal epithelial cells. BFP are polymers of bundlin and nine bundlin alleles have been identified in EPEC isolated from diverse sources. These alleles are divided into two main groups, α and β, based on their amino acid sequences. Alpha bundlins are also N‐acetyllactosamine‐ (LacNAc) specific lectins and bind to HEp‐2 cells, whereas β bundlins do not display these characteristics. The four surface‐exposed regions of amino acid sequence heterogeneity between α and β bundlin were therefore investigated as potential LacNAc‐specific carbohydrate‐binding domains in a bundlin. Mutation of one of these domains, 137‐GENNI‐141, in α1 bundlin to that of β bundlin (136‐SPDST‐140) resulted in BFP that no longer bound to LacNAc or HEp‐2 cells. Conversely, mutating the β3 bundlin gene to encode the α bundlin sequence at this domain resulted in the gain of HEp‐2 cell adherence. The importance of this domain in carbohydrate binding is supported by the finding that introducing the mutation GENNI→GENNT altered the α1 bundlin carbohydrate‐binding specificity from LacNAc to the Lewis X glycan sequence.
Dissection of recognition determinants of Escherichia coli	σ32 suggests a composite −10 region with an ‘extended −10’ motif and a core −10 element
Authors: Koo Byoung‐Mo , Rhodius Virgil A. , Campbell Elizabeth A. , Gross Carol A.
Published: April 2009

σ32 controls expression of heat shock genes in Escherichia coli and is widely distributed in proteobacteria. The distinguishing feature of σ32 promoters is a long −10 region (CCCCATNT) whose tetra‐C motif is important for promoter activity. Using alanine‐scanning mutagenesis of σ32 and in vivo and in vitro assays, we identified promoter recognition determinants of this motif. The most downstream C (−13) is part of the −10 motif; our work confirms and extends recognition determinants of −13C. Most importantly, our work suggests that the two upstream Cs (−16, −15) constitute an ‘extended −10’ recognition motif that is recognized by K130, a residue universally conserved in β‐ and γ‐proteobacteria. This residue is located in the α‐helix of σDomain 3 that mediates recognition of the extended −10 promoter motif in other σs. K130 is not conserved in α‐ and δ‐/ε‐proteobacteria and we found that σ32 from the α‐proteobacterium Caulobacter crescentus does not need the extended −10 motif for high promoter activity. This result supports the idea that K130 mediates extended −10 recognition. σ32 is the first Group 3 σ shown to use the ‘extended −10’ recognition motif.
Mutational analysis of Escherichia coli	σ28 and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element
Authors: Koo Byoung‐Mo , Rhodius Virgil A. , Campbell Elizabeth A. , Gross Carol A.
Published: April 2009

σ28 controls the expression of flagella‐related genes and is the most widely distributed alternative σ factor, present in motile Gram‐positive and Gram‐negative bacteria. The distinguishing feature of σ28 promoters is a long −10 region (GCCGATAA). Despite the fact that the upstream GC is highly conserved, previous studies have not indicated a functional role for this motif. Here we examine the functional relevance of the GCCG motif and determine which residues in σ28 participate in its recognition. We find that the GCCG motif is a functionally important composite element. The upstream GC constitutes an extended −10 motif and is recognized by R91, a residue in Domain 3 of σ28. The downstream CG is the upstream edge of −10 region of the promoter; two residues in Region 2.4, D81 and R84, participate in its recognition. Consistent with their role in base‐specific recognition of the promoter, R91, D81 and D84 are universally conserved in σ28 orthologues. σ28 is the second Group 3 σ shown to use an extended −10 region in promoter recognition, raising the possibility that other Group 3 σs will do so as well.