bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of TACC proteins with the FHL family: implications for ERK signaling
Authors: Lauffart Brenda , Sondarva Gautam V. , Gangisetty Omkaram , Cincotta Melissa , Still Ivan H.
Published: March 2007

The Transforming acidic coiled coil (TACC) proteins play a conserved role in normal development and tumorigenesis through interactions with multiple complexes involved in transcription, translation, and centrosomal dynamics. However, despite significant work on the function of TACC3 in the control of centrosomal mechanics, relatively little functional data is known about the family’s founding member, TACC1. From a continued analysis of clones isolated by an unbiased yeast two‐hybrid assay, we now show direct physical interactions between the TACC1 and the FHL (Four and a Half LIM‐only) family of proteins. The authenticity of these interactions was validated both in vitro and in cellular systems. The FHLs exhibit diverse biological roles such as the regulation of the actin cytoskeleton and are promiscuous coregulators for several transcription factors. The interaction of the endogenous TACC‐FHL proteins is primarily localized to the nucleus. However, similar to FHL2, overexpression of TACC1A in HEK293 is able to sequester serum activated ERK to the cytoplasm. This has the effect of reducing the serum induced transcriptional response of the c‐fos and c‐jun genes. The observation that TACCs can interact with the FHLs and alter their serum induced activities raises the possibility that the TACCs participate in crosstalk between cell signaling pathways important for cancer development and tumor progression. The transforming acidic coiled coil genes are known to be important prognostic indicators for breast, ovarian and lung cancer. In this manuscript, we identify a novel interaction between the TACCs and the FHL protein family. This interaction has an affect on ERK and may in part explain the variable associations and changes in subcellular locations of each family with specific subtypes of malignancy.
The 5′ untranslated regions (UTRs) of CCN1, CCN2, and CCN4 exhibit cryptic promoter activity
Authors: Huang Bau‐Lin , Dornbach Lisa M. , Lyons Karen M.
Published: March 2007

CCNs are structurally related matricellular proteins that are highly expressed in many embryonic and adult tissues, including the skeletal system and tumors, where canonical cap‐dependent translation is suppressed under hypoxic environments. CCNs are encoded by mRNAs containing long G/C rich 5′‐untranslated regions (5′‐UTRs). Given that they are expressed under conditions of cellular stress, it has been suggested that the long G/C‐rich regions contain internal ribosomal entry sites (IRES) that allow these mRNAS to be translated under conditions where cap‐dependent translation is suppressed. Previously published work supported this possibility. However, recent studies have shown that a number of previously reported cellular IRES elements do not in fact possess IRES activity. Here we aimed to reveal whether the 5′UTRs of CCNs harbor IRES activities. The 5′UTRs of CCN1, 2, and 4 were tested in this study. Our results showed that the 5′UTRs of these genes do not contain IRES elements, but instead appear to contain cryptic promoters. Both promoterless and hairpin‐containing dicistronic tests showed that transcription was initiated by cryptic promoter elements in 5′UTRs of CCN1, 2, and 4. When dicistronic mRNAs were translated in vitro or in vivo, no IRES activities were detected in the 5′UTRs of CCN1, 2, and 4. Furthermore, these cryptic promoter activities from 5′UTRs of CCN1, 2, and 4 could be detected in various cell types, including chondrocytes, osteoblasts, and endothelial cells, where the cryptic promoter permitted varying degrees of activation. In addition, the core promoter element of the CCN2 5′UTR was identified. CCNs are expressed under conditions of cellular stress, and it has been suggested that some CCN family members utilize IRES‐mediated translation initiation to facilitate this expression. We found no evidence for IRES activity, but rather found that the unusually long 5′UTRs of CCNs 1, 2, and 4 harbor cryptic promoters that showed varying degrees of activity in different cell types. These results suggest that these promoters may contribute to the regulation of CCN genes in vivo.
The clients and functions of Spanish university programmes for older people: a sociological analysis
Authors: ALFAGEME ALFREDO
Published: March 2007

‘University programmes for older people’ (UPOP) have recently expanded rapidly in Europe and are now well established. This study examines the functions and achievements of the programmes and the characteristics of UPOP students in Spain. The evaluation is from a general sociological perspective, and uses data from a survey of a representative sample of the students and other sources. The main socio-demographic findings are that the students are relatively young older people, have a relatively high socio-economic level, and are predominantly women and retired. It is shown that beyond the education imparted, the programmes also fulfil important social roles. A critical analysis of the programmes as social policy highlights their socially selective reach and impacts, and compares their actual and potential functions. Some alternatives are discussed. If UPOP are to maintain their identity as programmes for older people, a different approach is required to reach all elderly people, including the ‘really old’. On the other hand, if the objectives emphasise the promotion of social integration and personal development (in matters other than employment skills), there is no reason why they should be addressed exclusively to people aged 50 or more years (or any arbitrary age). Rather, they should be open to adults of all ages. If this change were made, UPOP would give less reinforcement to a particular social construction of old age.
Constructions of frailty in the English language, care practice and the lived experience
Authors: GRENIER AMANDA
Published: March 2007

The way frailty is conceptualised and interpreted has profound implications for social responses, care practice and the personal experience of care. This paper begins with an exegesis of the concept of frailty, and then examines the dominant notions of frailty, including how ‘frailty’ operates as a ‘dividing-practice’ through the classification of those eligible for care. The definitions and uses of ‘frailty’ in three discursive locations are explored in: (a) the Oxford English Dictionary, (b) the international research literature, and (c) older women's accounts of their lived experience. Three distinctive discourses are found, and applying a Foucauldian analysis, it is shown that the differences reflect overlaps and tensions between biomedical concepts and lived experiences, as well as negative underlying assumptions and ‘subjugated knowledge’. The concept of frailty represents and orders the context, organisational practices, social representations and lived experiences of care for older people. The evidence suggests that if, as the older women's accounts recommended, socially- and emotionally-located expressions of frailty were recognised in addition to the existing conceptions of risk of the body, frailty might no longer be thought of primarily as a negative experience of rupture and decline. To encourage this change, it is suggested that practice focuses on the prevention of frailty and associated feelings of loss, rather than reinforcing the feelings and experiences which render a person ‘frail’.
Real-time epidemic forecasting for pandemic influenza
Authors: HALL I. M. , GANI R. , HUGHES H. E. , LEACH S.
Published: March 2007

The ongoing worldwide spread of the H5N1 influenza virus in birds has increased concerns of a new human influenza pandemic and a number of surveillance initiatives are planned, or are in place, to monitor the impact of a pandemic in near real-time. Using epidemiological data collected during the early stages of an outbreak, we show how the timing of the maximum prevalence of the pandemic wave, along with its amplitude and duration, might be predicted by fitting a mass-action epidemic model to the surveillance data by standard regression analysis. This method is validated by applying the model to routine data collected in the United Kingdom during the different waves of the previous three pandemics. The success of the method in forecasting historical prevalence suggests that such outbreaks conform reasonably well to the theoretical model, a factor which may be exploited in a future pandemic to update ongoing planning and response.
First‐principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle
Authors: Wan J. T. K. , Duffy T. S. , Scandolo S. , Car R.
Published: March 2007

Constant‐pressure constant‐temperature ab initio molecular dynamics simulations at high temperatures have been used to study MgSiO3, the major constituent of the Earth's lower mantle to conditions of the Earth's core‐mantle boundary. The calculated equilibrium volumes and densities are compared with simulations using an orthorhombic perovskite configuration under the same conditions. For molten MgSiO3, we have determined the diffusion coefficients and shear viscosities at different thermodynamic conditions. Our results provide new constraints on the properties of molten MgSiO3 at conditions near the core‐mantle boundary. The volume of the liquid is greater than that of the solid throughout the pressure‐temperature conditions examined, and the volume change on fusion ranges from 5% at 88 GPa and 3500 K to 2.9% at 120 GPa and 5000 K. Existing experimental constraints on solid‐liquid partition coefficients for Fe suggest that Fe is preferentially partitioned into the liquid. Such enrichment of Fe increases the density of the liquid, thus allowing the possibility of negatively buoyant melts from (Mg,Fe)SiO3 perovskite compositions at deep lower mantle conditions for plausible values of solid‐liquid partition coefficients for Fe. At 120 GPa and 4500–5000 K, the diffusion coefficient of liquid MgSiO3 is 2–3 × 10−5 cm 2/s and the diffusion rates of the different chemical species are similar. The shear viscosity is estimated using Zwanzig's formula to be 19–31 cP under these conditions. On the basis of our calculated diffusivities, MgSiO3 is above the glass transition temperature at 120 GPa and 4500 K.
Separation of paramagnetic and ferrimagnetic anisotropies: A review
Authors: Martín‐Hernández Fátima , Ferré Eric C.
Published: March 2007

The magnetic anisotropy of rocks results from the contributions of diamagnetic, paramagnetic, and ferromagnetic (in the broad sense) minerals. This bulk anisotropy of magnetic susceptibility, which can be rapidly measured with modern instruments, generally provides a better understanding of the rock deformation history. Different minerals in a rock can form at different times and also respond to deformation in different manners. Therefore it is useful to separate their respective contributions to the whole rock magnetic fabric. Various techniques available to achieve this separation are presented and compared in this article. The variations of magnetic susceptibility with temperature can be used to selectively characterize the contribution of paramagnetic mineral phases following the Curie‐Weiss law. The measurement of magnetic remanence‐related anisotropy provides an efficient way to characterize the contribution of ferrimagnetic and antiferromagnetic species. Finally, measurement of the magnetic properties at high fields, above the saturation magnetization of ferromagnetic minerals, effectively separates the diamagnetic‐paramagnetic magnetic anisotropy. The recent development of these techniques allows the separation of paramagnetic and ferrimagnetic anisotropies to be performed routinely on most specimens and shows promising potential for future magnetic anisotropy studies.
Forecast experiment: Do temporal and spatial b value variations along the Calaveras fault portend M ≥ 4.0 earthquakes?
Authors: Parsons Tom
Published: March 2007

The power law distribution of earthquake magnitudes and frequencies is a fundamental scaling relationship used for forecasting. However, can its slope (b value) be used on individual faults as a stress indicator? Some have concluded that b values drop just before large shocks. Others suggested that temporally stable low b value zones identify future large‐earthquake locations. This study assesses the frequency of b value anomalies portending M ≥ 4.0 shocks versus how often they do not. I investigated M ≥ 4.0 Calaveras fault earthquakes because there have been 25 over the 37‐year duration of the instrumental catalog on the most active southern half of the fault. With that relatively large sample, I conducted retrospective time and space earthquake forecasts. I calculated temporal b value changes in 5‐km‐radius cylindrical volumes of crust that were significant at 90% confidence, but these changes were poor forecasters of M ≥ 4.0 earthquakes. M ≥ 4.0 events were as likely to happen at times of high b values as they were at low ones. However, I could not rule out a hypothesis that spatial b value anomalies portend M ≥ 4.0 events; of 20 M ≥ 4 shocks that could be studied, 6 to 8 (depending on calculation method) occurred where b values were significantly less than the spatial mean, 1 to 2 happened above the mean, and 10 to 13 occurred within 90% confidence intervals of the mean and were thus inconclusive. Thus spatial b value variation might be a useful forecast tool, but resolution is poor, even on seismically active faults.
A climatology of the northern Adriatic Sea's response to bora and river forcing
Authors: Jeffries Marlene A. , Lee Craig M.
Published: March 2007

A new northern Adriatic climatology characterizes salinity and temperature fields associated with response to strong riverine input and bora wind forcing acting on variable ambient stratification. Time series of key forcing variables, specifically Po River discharge and wind velocity in bora pathways, combined with a measure of time‐variable ambient stratification, indicate the dominant dynamics (e.g., bora winds acting on an unstratified northern Adriatic or strong Po River outflow into an unstratified basin). These indicators define an averaging scheme which organizes archived temperature and salinity profiles into groupings based on common dynamics, providing climatological characterizations of response to bora forcing and the differing basin responses to strong and weak Po discharge into strong and weak ambient stratification. The resulting maps demonstrate that the offshore penetration of Po waters depends strongly on outflow strength and ambient stratification. The climatology reveals buoyant Po River waters spreading in a surface layer throughout much of the northern basin during periods of strong ambient stratification, with little dependence on outflow strength. In contrast, during unstratified periods, outflow strength determines whether the river waters penetrate into the basin (strong outflow) or remain trapped over the Italian shelf (weak outflow). In addition, separation of oceanographic data into periods of strong bora winds reveals the formation of a freshwater filament in the resulting salinity fields. This feature extends into the open sea, separating two pools of higher salinity water. Significance testing of the mode‐maps with climatological averages indicate that the mode‐based maps are statistically robust within the 95% confidence interval in areas of energetic mesoscale activity such as those regions subject to direct riverine or wind forcing.
Dynamics of CD4+T cells in HIV‐1 infection
Authors: Ribeiro Ruy M
Published: March 2007

Mathematical modeling is becoming established in the immunologist's toolbox as a method to gain insight into the dynamics of the immune response and its components. No more so than in the case of the study of human immunodeficiency virus (HIV) infection, where earlier work on the viral dynamics brought significant advances in our understanding of HIV replication and evolution. Here, I review different areas of the study of the dynamics of CD4+T cells in the setting of HIV, where modeling played important and diverse roles in helping us understand CD4+T‐cell homeostasis and the effect of HIV infection. As the experimental techniques become more accurate and quantitative, modeling should play a more important part in both experimental design and data analysis.
Ambipolar charge carrier transport in mixed organic layers of phthalocyanine and fullerene
Authors: Opitz Andreas , Bronner Markus , Brütting Wolfgang
Published: March 2007

Mixed layers of copper-phthalocyanine (p-conductive) and fullerene (n-conductive) are used for the fabrication of organic field-effect transistors (OFET) and inverters. Regarding the electrical characteristics of these donor-acceptor blends they show ambipolar charge carrier transport, whereas devices made from only one of the materials show unipolar behavior. Such mixed films are model systems for ambipolar transport with adjustable field-effect mobilities for electrons and holes. By variation of the mixing ratio it is possible to balance the transport of both charge-carrier types. In this paper we discuss the variation of mobility and threshold voltage with the mixing ratio and demonstrate ambipolar inverters as a leadoff application. The gained results were analyzed by simulations using an analytical model for ambipolar transistors and subsequently compared to complementary inverters.
Size dependence of static and dynamic magnetic properties in nanoscale square Permalloy antidot arrays
Authors: Yu Minghui , Malkinski Leszek , Spinu Leonard , Zhou Weilie , Whittenburg Scott
Published: March 2007

Permalloy antidot arrays with different square hole sizes (1200×1200, 800×800, and 400×400nm2) have been fabricated by means of electron-beam lithography and lift-off techniques. The smaller square hole size results in enhanced remanence and reduced coercivity in the antidot array. Multiple resonance modes were clearly observed for the magnetic field applied normal to the array plane, and double uniform resonance modes occurred when the field deviated more than 30° from the normal to the plane. Two distinct dipolar field patterns with different orientations and magnitudes split the uniform resonance into double resonance modes. The double resonance modes show uniaxial in-plane anisotropy and the easy axes are orthogonal. The magnitude of the induced dipolar anisotropy remains almost constant with changes in the square hole size. The double resonance peaks move to low field with reduction of the square hole size.
Ultrafast magnetization dynamics in high perpendicular anisotropy [Co∕Pt]n multilayers
Authors: Barman Anjan , Wang Suqin , Hellwig Olav , Berger Andreas , Fullerton Eric E. , Schmidt Holger
Published: March 2007

We present time-resolved magneto-optical Kerr effect measurements of picosecond laser induced precessional dynamics in out-of-plane magnetized [Co(4Å)∕Pt(8Å)]n multilayer films. A fast precession of magnetization (up to 81GHz) emerges 6ps after pumping and decays within a 100ps time scale. The uniform precessional frequency was studied for varying external magnetic bias field and number of Co∕Pt repeats n. The variation of the precession frequency with external bias field is quantitatively understood using the macrospin model of the Landau-Lifshitz-Gilbert equation of motion [Phys. Z. Sowjetunion 8, 153 (1935); Phys. Rev. 100, 1243 (1955)], yielding a large perpendicular anisotropy of up to 1.0×107ergs∕cm3 for our samples. The precession frequency increases sharply with reduced n and almost saturates below n=5, suggesting a commensurate variation of the perpendicular anisotropy. A heavy damping of the precessional motion is observed with increasing n and can be explained by enhanced spin-orbit coupling in ultrathin films and interfacial effects.
Theoretical calculation of the low laying electronic states of the molecule NaCs with spin-orbit effect
Authors: Korek M. , Bleik S. , Allouche A. R.
Published: March 2007

The potential energy curves have been calculated for the 59 lowest electronic states of the molecule NaCs including the spin-orbit effect within the range of 4.5a0–20.0a0 of the internuclear distance R. Using an ab initio method, the calculation is based on a nonempirical pseudopotentials which take into consideration the spin-orbit effect. Gaussian basis sets have been used for both atoms, and the spin-orbit effects have been taken into consideration. The spectroscopic constants have been calculated for 56 electronic states. The components of the spin-orbit splitting have been identified for the states (1,2,4)Π3. The comparison of the present results with those available in the literature shows a very good agreement.
Three-dimensional simulation model of switching dynamics in phase change random access memory cells
Authors: Kim Dae-Hwang , Merget Florian , Först Michael , Kurz Heinrich
Published: March 2007

Switching dynamics associated with reset and set operations of vertical phase change random access memory (PCRAM) cells are studied using a three-dimensional simulation model. Based on a finite difference method, the numerical algorithm simulates the electrical, thermal, and phase change dynamics in the PCRAM device during switching operations taking into account electrical and thermal percolation characteristics of the phase change material. Toward a better understanding of switching operations and the optimization of cell designs, the obtained simulation results provide unprecedented insight into temporally and spatially resolved kinetics of device temperature, current densities, and phase transitions. Threshold conditions for reset and set operations are identified in close agreement to existing experimental data, and the scaling ability of the investigated vertical PCRAM cell design to a minimum feature size of at least 40 nm is demonstrated.
Detection of weak (∼0.5–300nT), low frequency (5–100Hz) magnetic fields at room temperature by kilohertz modulation of the magneto-optical hysteresis in rare earth–iron garnet films
Authors: Hafez J. M. , Gao J. , Eden J. G.
Published: March 2007

Periodic magnetic fields with frequencies in the 5–100Hz range and peak strengths as low as 0.5nT have been detected at 300K by modulating at kHz rates the magneto-optical response of epitaxial (Tm,Bi)3(Ga,Fe)5O12 rare earth–iron garnet films at λ=532nm. By exploiting the ∼1°∕μT slope of the magneto-optical transition region between the two magnetization states of these low coercivity (<0.5mT) films, sub-nT field strengths can be measured by upconverting the detection process into the kHz domain. The domain wall velocities are measured to be 3–30m∕s for modulation frequencies in the 0.3–10kHz interval, and the noise generated by wall motion appears to be the primary barrier to further reductions in the detection sensitivity floor. Films with thicknesses of 2–4μm and mean domain widths of 3–6mm exhibit figures of merit (Θ∕α) of ∼3°–8.5° at 532nm. Imaging of mesoscopic magnetic particles is demonstrated with a spatial resolution of <300μm.
Giant third-order nonlinearity of lead and germanium based films in the visible and in the infrared
Authors: de Araújo Cid B. , Humeau A. , Boudebs G. , Del Cacho Vanessa D. , Kassab Luciana R. P.
Published: March 2007

The nonlinearity of lead and germanium based films with thickness of 1.5μm was studied using a mode-locked picosecond Nd:YAG laser at 1064nm and its second harmonic at 532nm. Nonlinear refractive indices of ≈10−16m2∕W and two-photon absorption coefficients varying from ≈102cm∕GW at 1064nmto≈103cm∕GW at 532nm were measured. The results show that the films have potential applications in optical limiting devices.
Schottky barrier modulation on silicon nanowires
Authors: Piscator J. , Engström O.
Published: March 2007

Oxide charge on the sidewalls of SiO2 embedded silicon wires with 20×20nm2 cross section is shown to influence the Schottky barrier height for Pd2Si∕Si junctions positioned on the end surfaces of the wires. Compared with results on planar silicon surfaces, the electron barrier height is 0.3eV lower for wires investigated as fabricated. By increasing the oxide charge through irradiation by ultraviolet light, the electron barrier decreases by an additional 0.15eV and the hole barrier correspondingly increases by about the same amount. The phenomenon is explained by assuming an oxide charge density in the range of 1012cm−2.
X-ray photoemission study of CoFeB∕MgO thin film bilayers
Authors: Read J. C. , Mather P. G. , Buhrman R. A.
Published: March 2007

The authors present results from an x-ray photoemission spectroscopy study of CoFeB∕MgO bilayers where they observe process-dependent formation of B, Fe, and Co oxides at the CoFeB∕MgO interface due to oxidation of CoFeB during MgO deposition. Vacuum annealing reduces the Co and Fe oxides but further incorporates B into the MgO forming a composite MgBxOy layer. Inserting an Mg layer between CoFeB and MgO introduces an oxygen sink, providing increased control over B content in the barrier.
Saturation and intrinsic dynamics of fluxons in NbTi and MgB2
Authors: Chamberlin R. V. , Newman N. , Gandikota R. , Singh R. K. , Moeckly B. H.
Published: March 2007

The authors measured the remanent magnetization of superconducting NbTi and MgB2 as a function of time after removing an applied field. At similar reduced temperatures, the density of magnetic flux quanta (fluxons) is found to relax faster in NbTi than in MgB2. Nearer the transition, the relaxation rate in both materials exhibits a saturation that is independent of the initially applied field. This saturation occurs when the distance between fluxons is comparable to the London penetration depth. The temperature dependence of the saturation and time dependence of the relaxation can be characterized by the Anderson-Kim model [Rev. Mod. Phys. 36, 39 (1964)] for fluxon dynamics.
Well-width-dependent carrier lifetime in AlGaN∕AlGaN quantum wells
Authors: Mickevičius J. , Tamulaitis G. , Kuokštis E. , Liu K. , Shur M. S. , Zhang J. P. , Gaska R.
Published: March 2007

A set of Al0.35Ga0.65N∕Al0.49Ga0.51N multiple quantum wells (MQWs) with fixed barrier width and well widths varying from 1.65to5.0nm has been grown by metal-organic chemical vapor deposition. Carrier dynamics in the MQWs were studied using time-resolved photoluminescence (PL) spectroscopy and light-induced transient grating (four wave mixing) technique. The authors observed that the lifetime of nonequilibrium carriers (excitons) increases with decreasing well width and interpreted the effect by stronger localization preventing their migration to nonradiative recombination centers. Meanwhile the radiative decay time is also influenced by screening of the built-in electric field, which spatially separates the electrons and holes. It is shown that this effect affects the initial part of PL intensity decay after pulsed excitation. It becomes more pronounced with increase in the initial carrier density but saturates when the carrier density is high enough to completely screen the built-in electric field. The screening effect on PL decay is stronger in wider quantum wells.
Surface recombination velocity in GaAs and In0.15Ga0.85As thin films
Authors: Brammertz Guy , Heyns Marc , Meuris Marc , Caymax Matty , Jiang Dehuai , Mols Yves , Degroote Stefan , Leys Maarten , Borghs Gustaaf
Published: March 2007

The authors have made photoluminescence intensity (PLI) measurements on thin GaAs and InGaAs films to compare the surface recombination velocity at interfaces of the materials with AlAs and native oxide. An analytical expression for the internal quantum efficiency of the PLI method for thin semiconducting films is derived. This expression is applied to measurements on specially designed multilayer structures based on GaAs and InGaAs thin films. The results show that the native oxide on an In0.15Ga0.85As film has a one order of magnitude lower surface recombination velocity than the native oxide on a GaAs film.
Estimating the sustained swimming ability of coral reef fishes
Authors: Johansen J. L. , Fulton C. J. , Bellwood D. R.
Published: March 2007

Sustained swimming ability can play a critical role in the ecology of fishes, particularly in terms of their distribution among habitats of differing flow conditions. However, the relative utility of various measures of swimming ability remains to be determined. The present study assessed the swimming speed performances of coral reef fishes using a range of experimental methods. This included a novel technique that measures the speed at which labriform fishes change gait from purely pectoral to pectoral-and-caudal propulsion over sustained time scales of >200 min (termed Up–nE). Measures of Up–cE were compared with two commonly used experimental metrics: critical swimming speed (Ucrit) and critical transition speed (Up–c). All three methods revealed consistent differences among taxa, and provided a reliable means of comparing swimming speed performances. Notably, two experimental measures (Up–c and Up–cE) appeared to more closely reflect the swimming speeds displayed by the same coral reef fishes in the field.
A decline in the abundance and condition of a native bivalve associated with Caulerpa taxifolia invasion
Authors: Wright Jeffrey T. , McKenzie Louise A. , Gribben Paul E.
Published: March 2007

Caulerpa taxifolia is a fast-spreading invasive seaweed that threatens biodiversity in temperate Australian estuaries. To date, little is known about its effects on infauna. In the present study, we describe variation in demographic and life-history traits of the abundant infaunal bivalve, Anadara trapezia, in C. taxifolia and uninvaded habitats (seagrass and unvegetated sediments) at multiple sites across three estuaries in south-eastern New South Wales. Densities of A. trapezia were always lower in C. taxifolia than on unvegetated sediment, and lower in C. taxifolia than in seagrass at three out of four sites where they were compared. Dry tissue weight of A. trapezia was also lower in C. taxifolia than on unvegetated sediment at most sites, but was only lower in C. taxifolia than in seagrass at one of four sites. Populations were dominated by larger individuals (>45 mm length), but smaller individuals (35–45 mm length) were more common in C. taxifolia and seagrass. A. trapezia shell weight and morphology was variable and appeared weakly affected by invasion. Generally, our findings are consistent with the hypothesis that A. trapezia is negatively affected by C. taxifolia. However, C. taxifolia invasion appears complex and, at some places, its effects may not differ from those of native seagrass. There is a need for manipulative studies to understand the mechanisms underlying the effects of C. taxifolia on infauna.
Mind the gap: did Darwin avoid publishing his theory for many years?
Authors: van Wyhe John
Published: March 2007

It is widely believed that Charles Darwin avoided publishing his theory of evolution for many years. Many explanations have been proposed to identify Darwin's reasons or motives for doing so. This essay demonstrates that Darwin's delay is a recent historiographical theme for which there is no clear evidence, and indeed is overwhelmingly contradicted by the historical evidence. It is also shown that Darwin's belief in evolution was not a secret before publication. Instead of a man afraid of his secret theory's being revealed to his prejudiced contemporaries, it is demonstrated that Darwin was understandably very busy and began his species book when he had completed work in hand, just as he had intended all along. This essay therefore rewrites a fundamental chapter in the story of Darwin's life and work as usually told.
Mentors, the marquise Du Châtelet and historical memory
Authors: Zinsser Judith P
Published: March 2007

When writing a biography, much has to be omitted to keep the life story focused and manageable for the reader. In
La Dame d'Esprit: a biography of the marquise Du Châtelet
the information about Émilie Du Châtelet's mentors seems, in retrospect, all too brief. This article therefore presents Maupertuis, Clairaut and Dortous de Mairan and describes their interactions with the marquise. It ends with speculations about why this exceptional
philosophe
is only now gaining the recognition she deserved as a member of France's eighteenth-century Republic of Letters.
The cane toad's (
Chaunus
[
Bufo
]
marinus
) increasing ability to invade Australia is revealed by a dynamically updated range model
Authors: Urban Mark C , Phillips Ben L , Skelly David K , Shine Richard
Published: March 2007

Invasive species threaten biological diversity throughout the world. Understanding the dynamics of their spread is critical to mitigating this threat. In Australia, efforts are underway to control the invasive cane toad (
Chaunus
[
Bufo
]
marinus
). Range models based on their native bioclimatic envelope suggest that the cane toad is nearing the end of its invasion phase. However, such models assume a conserved niche between native and invaded regions and the absence of evolution to novel habitats. Here, we develop a dynamically updated statistical model to predict the growing extent of cane toad range based on their current distribution in Australia. Results demonstrate that Australian cane toads may already have the ability to spread across an area that almost doubles their current range and that triples projections based on their native distribution. Most of the expansion in suitable habitat area has occurred in the last decade and in regions characterized by high temperatures. Increasing use of extreme habitats may indicate that novel ecological conditions have facilitated a broader realized niche or that toad populations at the invasion front have evolved greater tolerance to extreme abiotic conditions. Rapid evolution to novel habitats combined with ecological release from native enemies may explain why some species become highly successful global invaders. Predicting species ranges following invasion or climate change may often require dynamically updated range models that incorporate a broader realization of niches in the absence of natural enemies and evolution in response to novel habitats.
Invasibility in a spatiotemporally fluctuating environment is determined by the periodicity of fluctuations and resident turnover rates
Authors: Schoolmaster Donald R , Snyder Robin E
Published: March 2007

The ability of a species to invade a community is influenced by the traits of the invader, the resident community and the environment. However, qualitative generalizations are possible. Using a model of perennial plants in a spatiotemporally fluctuating environment, we find that fluctuating environments may be more or less invasible than static environments. Invasibility is strongly dependent on the interaction of the difference in turnover rates of resident and invader populations and the rate of temporal change of the environment. If resident population turnover is faster than the invader's, then invasibility is an initially positive, decreasing function of the period temporal variation, such that invasibility is increased by rapid temporal fluctuations but slightly reduced in slowly fluctuating environments. If resident turnover is slower than the invader's, then invasibility is an initially negative, increasing function of temporal period, such that invasibility is reduced in rapidly changing environment facilitated by slow temporal fluctuations. These results are explained by the relative abilities of resident and invader populations to successfully respond to environmental variation at different temporal scales.
Moraxella bovoculi sp. nov., isolated from calves with infectious bovine keratoconjunctivitis
Authors: Angelos John A. , Spinks Phillip Q. , Ball Louise M. , George Lisle W.
Published: March 2007

Eighteen isolates of a Gram-negative coccus (strain 237T) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; ‘pinkeye’) in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity. On the basis of 16S rRNA gene sequence, the isolates were most closely associated with Moraxella bovis and Moraxella ovis in clade I of the classical moraxellae. Biochemically, the novel isolates could be distinguished from the other members of the genus Moraxella isolated from animals on the basis of phenylalanine deaminase activity. The results of partial sequence analysis of six housekeeping genes, the 16S–23S rRNA gene interspacer region and partial 23S rRNA gene provide strong support for the inclusion of these isolates in a novel taxon, for which the name Moraxella bovoculi sp. nov. is proposed. The type strain is strain 237T (=ATCC BAA-1259T=CCUG 52049T).
Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Hoste Bart , Shin Dong Sung , Beleneva Irina A. , Vancanneyt Marc , Mikhailov Valery V.
Published: March 2007

The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221T, was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221Tis affiliated with the genusEchinicola, a member of the phylumBacteroidetes, with levels of similarity of 94.7–95.0 % to strains ofEchinicola pacifica. Growth of strain KMM 6221Twas observed with 0–15 % NaCl and at 6–44 °C. The DNA G+C content of strain KMM 6221Twas 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221Tis considered to represent a novel species of the genusEchinicola, for which the nameEchinicola vietnamensissp. nov. is proposed. The type strain is KMM 6221T(=DSM 17526T=LMG 23754T).
Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain
Authors: Zurdo-Piñeiro José Luis , Rivas Raúl , Trujillo Martha E. , Vizcaíno Nieves , Carrasco José Antonio , Chamber Manuel , Palomares Antonio , Mateos Pedro F. , Martínez-Molina Eustoquio , Velázquez Encarna
Published: March 2007

Two strains named ESC1T and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA–DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21T, O. anthropi DSM 6882T and Ochrobactrum tritici DSM 13340T. The predominant fatty acids were C18 : 1
ω7c and C18 : 1 2-OH. Strains ESC1T and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced β-galactosidase and β-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1T was 56.4 mol%. Both strains ESC1T and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1T (=LMG 22713T=CECT 7172T).
Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue
Authors: Endo Akihito , Okada Sanae
Published: March 2007

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.
Trabulsiella odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus Shiraki
Authors: Chou Jui-Hsing , Chen Wen-Ming , Arun A. B. , Young Chiu-Chung
Published: March 2007

Bacterial strains Eant 3-9T and Eant 3-3, isolated from the gut of the termite Odontotermes formosanus, were characterized using a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, non-pigmented, rod-shaped, non-endospore-forming and facultatively anaerobic. Phenotypic, physiological and genetic characteristics of the two strains were highly similar. Phylogenetic analyses using 16S rRNA gene sequences showed that strain Eant 3-9T formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Trabulsiella; its closest neighbour was Trabulsiella guamensis DSM 16940T (98.1 % similarity). Genomic DNA–DNA relatedness between strains Eant 3-9T and Eant 3-3 was 96±4 %, indicating that they belong to a single species. Eant 3-9T displayed DNA–DNA relatedness values of 48±5 and 14±3 % with T. guamensis DSM 16940T and Salmonella typhimurium ATCC 13311T, respectively, indicating that Eant 3-9T warrants novel species status in the genus Trabulsiella. Eant 3-9T and Eant 3-3 could be further distinguished from T. guamensis DSM 16940T using whole-cell protein profiles and a range of physiological and biochemical characteristics. It is evident from genotypic and phenotypic data that Eant 3-9T represents a novel species in the genus Trabulsiella, for which the name Trabulsiella odontotermitis sp. nov. is proposed. The type strain is Eant 3-9T (=BCRC 17577T=LMG 23580T); Eant 3-3 is a reference strain.
Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae
Authors: Gu Qiang , Paściak Mariola , Luo Hongli , Gamian Andrzej , Liu Zhiheng , Huang Ying
Published: March 2007

A Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6T, was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborderMicrococcineae. Its nearest phylogenetic neighbour was the type strain ofGeorgenia muralis(94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6Twere as follows: the major menaquinone was MK-8(H4); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0and iso-C16 : 0; mycolic acids were absent. A new murein type,l-lys–gly–l-glu–l-Glu (A4α), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6Trepresents a novel species of a new genus within the suborderMicrococcineae, for which the nameRuania albidiflavagen. nov., sp. nov. is proposed. The type strain ofRuania albidiflavais 3-6T(=CGMCC 4.3142T=DSM 18029T=JCM 13910T=PCM 2644T).
Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste
Authors: Young Chiu-Chung , Kämpfer Peter , Chen Wen-Ming , Yen Wen-Shao , Arun A. B. , Lai Wei-An , Shen Fo-Ting , Rekha P. D. , Lin Kuan-Yin , Chou Jui-Hsing
Published: March 2007

A yellow-pigmented, Gram-negative, rod-shaped bacterium (strain CC-YY255T) was isolated from compost generated from food waste collected from Kinmen County, Taiwan. 16S rRNA gene sequence analysis indicated that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Luteimonas; its closest neighbour was the type strain of Luteimonas mephitis (94.4 % sequence similarity). The isolate was distinguished from Luteimonas mephitis on the basis of several phenotypic properties. The organism utilized glucose, maltose, gentiobiose, melibiose and turanose and only a few organic acids (acetate, propionate) and amino acids (l-alanyl glycine, glycyl l-aspartic acid and glycyl l-glutamic acid) as substrates. The fatty acid profile was slightly different from that reported for Luteimonas mephitis. It is evident from the genotypic, chemotaxonomic and physiological data presented that strain CC-YY255T represents a novel species of the genus Luteimonas, for which the name Luteimonas composti sp. nov. is proposed. The type strain is CC-YY255T (=CCUG 53595T=CIP 109311T=BCRC 17598T).
Tamlana crocina gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae, isolated from beach sediment in Korea
Authors: Lee Soon Dong
Published: March 2007

A Gram-negative, aerobic, saffron-coloured marine bacterium, designated HST1-43T, was isolated from beach sediment on the coast in Jeju, Korea, and its taxonomic status was established in a polyphasic study. 16S rRNA gene sequence analyses revealed that the isolate belonged to the family Flavobacteriaceae. The closest phylogenetic neighbours of strain HST1-43T were members of the genera Algibacter, Gaetbulibacter and Yeosuana, with levels of sequence similarity in the range 96.3–96.5 %. The isolate was non-motile and required sea salts or natural seawater for growth. The optimum temperature and pH ranges for growth were 25–30 °C and pH 6.1–8.1, respectively. MK-6 was the major menaquinone. The dominant cellular fatty acids were iso-C15 : 0, C18 : 0, C16 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH. The DNA G+C content was 36.2±0.4 mol%. On the basis of phylogenetic distance and phenotypic characteristics, the isolate is considered to represent a novel genus and species in the family Flavobacteriaceae, for which the name Tamlana crocina gen. nov., sp. nov. is proposed. The type strain is HST1-43T (=KCTC 12721T=JCM 14021T).
Ignicoccus hospitalis sp. nov., the host of ‘Nanoarchaeum equitans’
Authors: Paper Walter , Jahn Ulrike , Hohn Michael J. , Kronner Michaela , Näther Daniela J. , Burghardt Tillmann , Rachel Reinhard , Stetter Karl O. , Huber Harald
Published: March 2007

A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for ‘Nanoarchaeum equitans’, the only cultivated member of the ‘Nanoarchaeota’. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/IT=DSM 18386T=JCM 14125T).