bluuebunny/crossref_metadata_2025 huggingface dataset:
Commissioning and performance of the variable line spacing plane grating monochromator beamline at the Canadian Light Source
Authors: Hu Y. F. , Zuin L. , Wright G. , Igarashi R. , McKibben M. , Wilson T. , Chen S. Y. , Johnson T. , Maxwell D. , Yates B. W. , Sham T. K. , Reininger R.
Published: August 2007

The variable line spacing plane grating monochromator beamline at the Canadian Light Source (CLS) employs three grazing incidence variable line spacing gratings to cover a photon energy range of 5–250eV. It uses a 185mm period length planar permanent magnet insertion device as the photon source, sharing a straight section with another soft x-ray beamline at the CLS. The commissioning and performance of the beamline is reported. The high resolution photoabsorption spectra of Ar and PF5 gases are reported. A resolving power of over 40 000 for photons in the low energy region and >10000 for a wider energy range (8–200eV) can be achieved. A photon flux of up to 2×1012photons∕sper100mA with slit settings of 50μm has been measured.
Nanoclustering of vacancies in thin metal films revealed by x-ray diffuse scattering
Authors: Kim Chinkyo , Feng Rui , Conrad Edward H. , Miceli Paul F.
Published: August 2007

The authors report the incorporation of unexpectedly large vacancy clusters into homoepitaxial Ag(001) films. These results, which are for a simple noble metal system, have important implications for understanding the atomic-scale kinetics of surfaces where current models have mostly ignored the role of vacancies. For films grown at 150 K, an average vacancy cluster exhibits a local dilatation volume of 750Å3, which leads to a 1% compressive strain of the film. Vacancy clusters are observed even for films grown near room temperature. These in situ diffuse x-ray scattering experiments measure the local deformation around the cluster and, therefore, provide conclusive evidence of vacancy clusters.
Experimental demonstration of a wavelength demultiplexer based on negative-refractive photonic-crystal components
Authors: Matsumoto Takashi , Asatsuma Tomohiko , Baba Toshihiko
Published: August 2007

Negative refraction of light was observed at near-infrared wavelengths in a silicon-on-insulator photonic-crystal-slab superprism having low-loss interface structures. It was used for wavelength demultiplexing as a diffraction grating, in combination with a photonic-crystal superlens used for focusing light beams. Coarse wavelength demultiplexing action with a channel spacing of 7–27nm was demonstrated in a device whose size was only 80×100μm2 (excluding input and output waveguides). These results agree well with those obtained by a finite-difference time-domain simulation.
Water excess under simulated lucerne - wheat phased systems in Western Australia
Authors: Dolling P. J. , Asseng S. , Robertson M. J. , Ewing M. A.
Published: August 2007

The long-term effect of lucerne use, in reducing drainage of water below the root zone and runoff (water excess), has not been examined in south-western Australia (Western Australia). The main aims of the paper were to determine how the long-term mean water excess was influenced by the proportion of lucerne in the rotation and the length of the lucerne phase in relation to soil type and location. A simulation model was used to compare scenarios, drawing on historical weather data from 1957 to 2001. Simulations were performed for 2 locations (high and low rainfall) and 2 soil types (high and low water-holding capacity).
Lucerne significantly and rapidly (within 2–3 years) reduces the long-term mean water excess in rotations consisting of 2–4 years of lucerne followed by 1–4 years of wheat compared with continuous wheat. For every 10% increase in the percentage of lucerne years in the total rotation length, the mean water excess decreased by 17–20 mm (7–9%) at Kojonup (high-rainfall site) and 7–8 mm (8–9%) at Buntine (low-rainfall site) compared with the water excess associated with continuous wheat at each location. The proportion of lucerne in the rotation had a greater effect on the water excess than the effect of different soil types. Variation in the water excess due to variation in rainfall was greater than the reduction in water excess due to lucerne. This makes the decisions about when to grow lucerne to reduce water excess difficult if livestock enterprises are less profitable than cropping enterprises. The simulations show that lucerne mean yearly biomass ranges from 4.5 to 6.9 t/ha at Kojonup and from 1.6 to 4.7 t/ha at Buntine, depending on soil type and stage of lucerne in the land use sequence. It is worth considering that lucerne has the potential to reduce subsequent wheat yields with removal in autumn.
Seed priming with brassinolide improves lucerne (Medicago sativa L.) seed germination and seedling growth in relation to physiological changes under salinity stress
Authors: Zhang S. , Hu J. , Zhang Y. , Xie X. J. , Knapp Allen
Published: August 2007

Salt stress is an important constraint to lucerne (Medicago sativa L.) production in many parts of the world. Seeds of 3 lucerne varieties, cvv. Victoria, Golden Empress, and Victor, were used to investigate the effects of seed priming with 5 µm/L brassinolide on germination and seedling growth under a high level of salt stress (13.6 dS/m NaCl solution). The results showed that germination percentage, germination index, and vigour index of lucerne seeds primed with brassinolide were significantly higher than those of the non-primed seeds under salinity stress in each variety. Seed priming with brassinolide significantly increased the shoot fresh weight, shoot dry weight, and root dry weight in 2 varieties, and significantly increased the root length and root vigour in each variety. It also significantly increased the activities of antioxidant enzymes, peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), in Victoria and Victor seedlings. During seedling growth, the primed seeds significantly reduced the malondialdehyde (MDA) accumulation. This suggests that priming lucerne seed with brassinolide at a suitable concentration can improve germination and seedling growth under high-saline soils.
QTL analysis of yield-related traits and their association with functional markers in Brassica napus L.
Authors: Li Yuanyuan , Shen Jinxiong , Wang Tonghua , Chen Qingfang , Zhang Xingguo , Fu Tingdong , Meng Jinling , Tu Jinxing , Ma Chaozhi
Published: August 2007

Yield is one of the most important traits in Brassica napus breeding programs. Quantitative trait loci (QTLs) for yield-related traits based on genetic mapping would help breeders to develop high-yield cultivars. In this study, a genetic linkage map of B. napus, containing 142 sequence-related amplified polymorphism (SRAP) markers, 163 functional markers, 160 simple sequence repeat (SSR) markers, and 117 amplified fragment length polymorphism (AFLP) markers, was constructed in an F2 population of 184 individuals resulting from the cross SI-1300 × Eagle. This map covered 2054.51 cM with an average marker interval of 3.53 cM. Subsequently, QTLs were detected for 12 yield-related traits in Wuhan and Jingmen. In total, 133 QTLs were identified, including 14 consistent ones across the 2 locations. Fifteen of 20 linkage groups (LGs) were found to have QTLs for the 12 traits investigated, and most of the QTLs were clustered, especially on LGs N2 and N7, where similar QTL positions were identified for multiple traits. Eight of 10 QTLs for yield per plant (YP) were also associated with number of seeds per silique (SS), number of siliques per plant (SP), and/or 1000-seed weight (SW). In addition, 45 functional markers involved in 39 expressed sequence tags (ESTs) were linked to the QTLs of 12 traits. The present results may serve as a valuable basis for further molecular dissection of agronomic traits in B. napus, and the markers related to QTLs may offer promising possible makers for marker assisted selection.
Gene mapping of brachytic stem and its effects on yield-related traits in soybean
Authors: Cui Shiyou , Meng Qingchang , Gai Junyi , Yu Deyue
Published: August 2007

Plant height, determinate growth habit, and brachytic stem are 3 major plant-type traits of soybean. In this report, a population of 151 recombinant inbred lines (RILs) derived from the cross of Bogao (high stature, indeterminate growth habit, and normal stem) and Nannong 94-156 (short stature, determinate growth habit, and brachytic stem) was used to map genes and quantitative trait loci (QTLs) for 3 plant-type traits and to reveal the effects of brachytic stem on yield-related traits including seed yield, apparent biological yield, apparent harvest index, plant height, and days to maturity. The results indicated that brachytic stem (sb) and determinate growth habit (dt1) were mapped on linkage groups B2 and L, respectively. Two major QTLs related to plant height were detected and mapped on linkage group L near dt1, and 0.6 cM above the Sb locus on linkage group B2 across 2 years. These 2 QTLs explained 15.1% and 52.7% of the phenotypic variation, and decreased plant height by 9.2 and 17.6 cm, respectively. It was found that only one QTL was detected and mapped on linkage group L near dt1 across 2 years. Lines with brachytic stem had shorter plant height, lower biomass, yield, and harvest index, and essentially no differences in days to maturity when compared with normal stem lines.
Molecular tagging of the male fertility restorer gene for the 501-8S cytoplasmic male sterility in rapeseed (Brassica napus L.)
Authors: He Haohua , Xu Liang , Peng Xiaosong , Yang Guangsheng , Zhu Changlan , Liu Zunwen , Ye Guoyou
Published: August 2007

The cytoplasmic male sterile (CMS) system has been successfully used to explore heterosis in rapeseed (Brassica napus L.). A newly developed male sterile line (501-8S) was characterised for its male fertility response to temperature and photoperiod, and the inheritance of fertility restoration. Segregation analysis using F1 and F2, BC1, and F3 populations of the crosses between the 501-8S and fertile lines of B. napus revealed that fertility restoration was conferred by a dominant nuclear gene (Rf). The F2 population of the cross 501-8S × Yuyou1 was used as a mapping population to map the Rf gene. A combination of bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) methodology was used to identify putative markers linked to the Rf gene. Twenty-nine of the 1280 primer combinations tested revealed polymorphism between the 2 extreme bulks. Further testing of these primer combinations in individual plants identified 5 AFLP markers tightly linked to the Rf gene with a map distance of less than 5.0 cM. All 5 markers were on one side of the restoration gene in the coupling phase. The closest marker, EA02MG03-260, is only 0.4 cM from the Rf gene. The EA02MG03-260 marker was converted to a dominant sequence characterised amplified region (SCAR) marker (SCARE2M3-214). Amplification using this locus-specific primer generated specific bands with male fertile plants when tested using the mapping population. Specific amplification of SCARE2M3-214 was also detected in all 3 male sterile plants and their F1 hybrids, with 5 restorer lines used for verification. Thus, SCARE2M3-214 will be very useful for the development of new restorer lines by the transfer of the Rf gene into other breeding lines. It can also be used for isolating the Rf gene by means of map-based cloning.
Genomics, biogeography, and the diversification of placental mammals
Authors: Wildman Derek E. , Uddin Monica , Opazo Juan C. , Liu Guozhen , Lefort Vincent , Guindon Stephane , Gascuel Olivier , Grossman Lawrence I. , Romero Roberto , Goodman Morris
Published: August 2007

Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not decisively resolved the basal branching order within Placentalia. Here, on extracting from thousands of gene loci both their coding nucleotide sequences and translated amino acid sequences, we attempt to resolve key uncertainties about the ancient branching pattern of crown placental mammals. Focusing on ≈1,700 conserved gene loci, those that have the more slowly evolving coding sequences, and using maximum-likelihood, Bayesian inference, maximum parsimony, and neighbor-joining (NJ) phylogenetic tree reconstruction methods, we find from almost all results that a clade (the southern Atlantogenata) composed of Afrotheria and Xenarthra is the sister group of all other (the northern Boreoeutheria) crown placental mammals, among boreoeutherians Rodentia groups with Lagomorpha, and the resultant Glires is close to Primates. Only the NJ tree for nucleotide sequences separates Rodentia (murids) first and then Lagomorpha (rabbit) from the other placental mammals. However, this nucleotide NJ tree still depicts Atlantogenata and Boreoeutheria but minus Rodentia and Lagomorpha. Moreover, the NJ tree for amino acid sequences does depict the basal separation to be between Atlantogenata and a Boreoeutheria that includes Rodentia and Lagomorpha. Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.
Ancient bacteria show evidence of DNA repair
Authors: Johnson Sarah Stewart , Hebsgaard Martin B. , Christensen Torben R. , Mastepanov Mikhail , Nielsen Rasmus , Munch Kasper , Brand Tina , Gilbert M. Thomas P. , Zuber Maria T. , Bunce Michael , Rønn Regin , Gilichinsky David , Froese Duane , Willerslev Eske
Published: August 2007

Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.
Narrative in adolescent specific language impairment (SLI): a comparison with peers across two different narrative genres
Authors: Wetherell Danielle , Botting Nicola , Conti‐Ramsden Gina
Published: August 2007

Background: Narrative may provide a useful way in which to assess the language ability of adolescents with specific language impairment and may be more ecologically valid than standardized tests. However, the language of this age group is seldom studied and, furthermore, the effect of narrative genre has not been explored in detail.

Methods & Procedures: A total of 99 typically developing adolescents and 19 peers with specific language impairment were given two different types of narrative task: a story‐telling condition and a conversational condition. Four areas of narrative (productivity, syntactic complexity, syntactic errors and performance) were assessed.

Outcomes & Results: The group with specific language impairment was poorer on most aspects of narrative confirming recent research that specific language impairment is a long‐term disorder. A number of measures also showed interactions between group and genre, with story‐telling proving to be a disproportionately more difficult task for the specific language impairment group. Error analysis also suggested that the specific language impairment group was making qualitatively different errors to the typically developing group, even within a genre.

Conclusions: Adolescents with specific language impairment are not only poorer at both types of narrative than peers, but also show different patterns of competence and error, and require more support from the narrative‐partner.

Clinical Implications: Assessments of adolescents are less frequent than at younger ages. This is partly because of the sparsity of tests available in this age range. Qualitative analysis of narrative might prove a useful alternative. The findings suggest that in every‐day conversation, young people with specific language impairment manage their difficulties more discreetly and this might make them harder to identify in a mainstream setting.
Analysis of formant frequencies in patients with oral or oropharyngeal cancers treated by glossectomy
Authors: Kazi Rehan , Prasad Vyas M. N. , Kanagalingam Jeeve , Georgalas Christos , Venkitaraman Ramachandran , Nutting Christopher M. , Clarke Peter , Rhys‐Evans Peter , Harrington Kevin J.
Published: August 2007

Aims: To compare voice quality as defined by formant analysis using a sustained vowel in patients who have undergone a partial glossectomy with a group of normal subjects.

Methods & Procedures: The design consisted of a single centre, cross‐sectional cohort study. The setting was an Adult Tertiary Referral Unit. A total of 26 patients (19 males) who underwent partial glossectomy and 31 normal volunteers (18 males) participated in the study. Group comparisons using the first three formant frequencies (F1, F2 and F3) using linear predictive coding (Laryngograph Ltd, London, UK) were performed. The existence of any significant difference of F1, F2 and F3 between the two groups using the sustained vowel /i/ and the effects of other factors, namely age, first presentation versus recurrence, site (oral cavity, oropharynx), subsite (anterior two‐thirds of the tongue, tongue base), stage, radiation, complication, and neck dissection, were analysed.

Outcomes & Results: Formant frequencies F1, F2 and F3 were normally distributed. F1 and F2 were significantly different in normal males versus females. F1, F2 and F3 were not different statistically between male and female glossectomees. Comparison of only women showed significant differences between normal subjects and patients in F2 and F3, but none in F1. This was the opposite in men where F1 was significantly different. Age, tumour presentation, site, subsite, radiation and neck dissection showed no significant difference. Postoperative complications significantly affected the F1 formant frequency.

Conclusions: The study found that the formant values in patients following a partial glossectomy were altered significantly as compared with the normal control subjects. Only gender and complications and not the age, site, subsite, radiation and neck dissection were seen to influence the formant scores.
Near infrared reflectography for deciphering obscured (whitewashed or ablated) epigraphs
Authors: Falcone L , Bloisi F , Califano V , Pagano M , Vicari L
Published: August 2007

Infrared reflectography (IRR) is a non-destructive imaging technique based on the different optical behaviour of visible and near infrared (NIR) radiation through a thin pictorial layer. This effect is a consequence of both lower NIR absorption and reduced NIR scattering due to the particle size smaller than the wavelength. Here we present an interesting and, to our knowledge, new application of this technique to ancient multi-layered epigraphs, showing its useful application in archaeology. Both tests on laboratory samples and preliminary tests on the field show that it is possible to use IRR taken with a vidicon wide spectral range camera (let us call this NIR reflectography (NIRR) to underline the wide spectral range including almost all NIR, but excluding thermal infrared radiation), to read inscriptions ‘deleted’ by means of a whitewashing layer. The field tests carried out on a multi-layer inscription ‘notice board’ in Herculaneum have shown that NIRR can also be useful in integrating some gaps of the currently visible layer inscription and in reconstructing the layout of the inscription wiped off by mechanical abrasion. All these applications are of much interest since ancient Greek and Latin public documents were frequently written with black pigment on whitewashed boards and ‘wiped off’ when the inscription was no more required.
Core electron-root confinement (CERC) in helical plasmas
Authors: Yokoyama M. , Maaßberg H. , Beidler C.D. , Tribaldos V. , Ida K. , Estrada T. , Castejon F. , Fujisawa A. , Minami T. , Shimozuma T. , Takeiri Y. , Dinklage A. , Murakami S. , Yamada H.
Published: August 2007

The improvement of core electron heat confinement has been realized in a wide range of helical devices such as CHS, LHD, TJ-II and W7-AS. Strongly peaked electron temperature profiles and large positive radial electric field,Er, in the core region are common features for this improved confinement. Such observations are consistent with a transition to the ‘electron-root’ solution of the ambipolarity condition forErin the context of neoclassical transport, which is unique to non-axisymmetric configurations. Based on this background, this improved confinement has been collectively dubbed ‘core electron-root confinement’ (CERC). The thresholds for CERC establishment are found for the collisionality and electron cyclotron heating power. The magnetic configuration properties (e.g. effective ripple and magnetic islands/rational surfaces) play important roles for CERC establishment.
Sustainment of FRC-equilibrium by use of a centre solenoid in TS-4
Authors: Kawamori E. , Sumikawa T. , Imanaka H. , Imazawa R. , Yamashita K. , Hayamizu T. , Ono Y.
Published: August 2007

This paper addresses a basic equilibrium/confinement question whether a field reversed configuration (FRC) with a balanced amount of magnetic and thermal energies is sustained solely by inductive magnetic flux (magnetic energy) injection of a centre solenoid coil. A new finding is that preferential injection of magnetic energy causes a significant increase in thermal energy of the FRC to maintain high-beta equilibrium. The FRC plasma is concluded to have the robustness needed to self-adjust the plasma heating power depending on the magnetic energy injection. In the flux ramped-up phase, i.e. in the phase where the applied inductive electric field did not penetrate into the core of the plasma, theJ×Bcompression (pinch effect) was considered to be dominant for heating the FRC. On the other hand, after the applied inductive electric field penetrated into the core region the resistivity of the FRC increased up to 10–20 times larger than the classical spitzer resistivity. This anomalous heating was the most probable cause for sustainment of the high-beta FRC in this phase. A quasi-steady state of the high-beta (volume averaged beta ∼0.6–0.7) FRC for 0.15 ms (∼energy confinement time of conventional FRCs) was achieved by the use of the present low power centre solenoid current drive. This successful result leads us to the next stage steady sustainment experiment of an FRC by increased capacitor bank energy.
Experiments and modelling of external kink mode control using modular internal feedback coils
Authors: Sunn Pedersen T. , Maurer D.A. , Bialek J. , Katsuro-Hopkins O. , Hanson J.M. , Mauel M.E. , James R. , Klein A. , Liu Y. , Navratil G.A.
Published: August 2007

We report on recent advances in modelling and experiments on resistive wall mode feedback control. The first experimental demonstration of feedback suppression of rotating external kink modes near the ideal wall limit in a tokamak is described [1]. This was achieved using an optimized control system employing a low latency digital controller and directly coupled modular feedback coils. The magnitude of plasma dissipation affecting kink mode behaviour has also been experimentally quantified for the first time using measurements of the radial eigenmode structure of the poloidal field fluctuations associated with the rotating kink mode. New capabilities of the VALEN code [2] are also reported. These include the ability to simulate multiple plasma modes and mode rotation in the model of the feedback control loop. Results from VALEN modelling of resistive wall mode feedback control in ITER are also presented, showing a significant improvement in performance with internal coils. Evidence for a lack of mode rigidity in HBT-EP is given, and plans to address this and other issues related to coil coverage and coil modularity are presented.
Observations of secondary structures after collapse events occurring at the q = 2 magnetic surface in the TEXTOR tokamak
Authors: Liang Y. , Koslowski H.R. , Krämer-Flecken A. , Zimmermann O. , Löwenbrück K. , Bertschinger G. , Wolf R.C.
Published: August 2007

Collapse events at theq= 2 surface occurring during the mode locking process of anm/n= 2/1 tearing mode have been observed on TEXTOR. The plasma confinement within theq= 2 surface collapses without much influence on the width of the island (O-point). With an external rotating resonant magnetic perturbation (RMP) field induced by the dynamic ergodic divertor, secondary structures moving near the separatrix of the primary large 2/1 island with the same frequency as the RMP have been observed after the collapse events. The plasma confinement recovers when the secondary structures vanish.
WNT10B Functional Dualism: β-Catenin/Tcf-dependent Growth Promotion or Independent Suppression with Deregulated Expression in Cancer
Authors: Yoshikawa Hirohide , Matsubara Kenichi , Zhou Xiaoling , Okamura Shu , Kubo Takahiko , Murase Yaeko , Shikauchi Yuko , Esteller Manel , Herman James G. , Wei Wang Xin , Harris Curtis C.
Published: August 2007

We found aberrant DNA methylation of the WNT10B promoter region in 46% of primary hepatocellular carcinoma (HCC) and 15% of colon cancer samples. Three of 10 HCC and one of two colon cancer cell lines demonstrated low or no expression, and 5-aza-2′deoxycytidine reactivated WNT10B expression with the induction of demethylation, indicating that WNT10B is silenced by DNA methylation in some cancers, whereas WNT10B expression is up-regulated in seven of the 10 HCC cell lines and a colon cancer cell line. These results indicate that WNT10B can be deregulated by either overexpression or silencing in cancer. We found that WNT10B up-regulated β-catenin/Tcf activity. However, WNT10B-overexpressing cells demonstrated a reduced growth rate and anchorage-independent growth that is independent of the β-catenin/Tcf activation, because mutant β-catenin–transduced cells did not suppress growth, and dominant-negative hTcf-4 failed to alleviate the growth suppression by WNT10B. Although WNT10B expression alone inhibits cell growth, it acts synergistically with the fibroblast growth factor (FGF) to stimulate cell growth. WNT10B is bifunctional, one function of which is involved in β-catenin/Tcf activation, and the other function is related to the down-regulation of cell growth through a different mechanism. We suggest that FGF switches WNT10B from a negative to a positive cell growth regulator.
PAR-3 and PAR-1 Inhibit LET-99 Localization to Generate a Cortical Band Important for Spindle Positioning inCaenorhabditis elegansEmbryos
Authors: Wu Jui-Ching , Rose Lesilee S.
Published: August 2007

The conserved PAR proteins are localized in asymmetric cortical domains and are required for the polarized localization of cell fate determinants in many organisms. In Caenorhabditis elegans embryos, LET-99 and G protein signaling act downstream of the PARs to regulate spindle positioning and ensure asymmetric division. PAR-3 and PAR-2 localize LET-99 to a posterior cortical band through an unknown mechanism. Here we report that LET-99 asymmetry depends on cortically localized PAR-1 and PAR-4 but not on cytoplasmic polarity effectors. In par-1 and par-4 embryos, LET-99 accumulates at the entire posterior cortex, but remains at low levels at the anterior cortex occupied by PAR-3. Further, PAR-3 and PAR-1 have graded cortical distributions with the highest levels at the anterior and posterior poles, respectively, and the lowest levels of these proteins correlate with high LET-99 accumulation. These results suggest that PAR-3 and PAR-1 inhibit the localization of LET-99 to generate a band pattern. In addition, PAR-1 kinase activity is required for the inhibition of LET-99 localization, and PAR-1 associates with LET-99. Finally, examination of par-1 embryos suggests that the banded pattern of LET-99 is critical for normal posterior spindle displacement and to prevent spindle misorientation caused by cell shape constraints.
Stress-activated Protein Kinase-mediated Down-Regulation of the Cell Integrity Pathway Mitogen-activated Protein Kinase Pmk1p by Protein Phosphatases
Authors: Madrid Marisa , Núñez Andrés , Soto Teresa , Vicente-Soler Jero , Gacto Mariano , Cansado José
Published: August 2007

Fission yeast mitogen-activated protein kinase (MAPK) Pmk1p is involved in morphogenesis, cytokinesis, and ion homeostasis as part of the cell integrity pathway, and it becomes activated under multiple stresses, including hyper- or hypotonic conditions, glucose deprivation, cell wall-damaging compounds, and oxidative stress. The only protein phosphatase known to dephosphorylate and inactivate Pmk1p is Pmp1p. We show here that the stress-activated protein kinase (SAPK) pathway and its main effector, Sty1p MAPK, are essential for proper deactivation of Pmk1p under hypertonic stress in a process regulated by Atf1p transcription factor. We demonstrate that tyrosine phosphatases Pyp1p and Pyp2p, and serine/threonine phosphatase Ptc1p, that negatively regulate Sty1p activity and whose expression is dependent on Sty1p-Atf1p function, are involved in Pmk1p dephosphorylation under osmostress. Pyp1p and Ptc1p, in addition to Pmp1p, also control the basal level of MAPK Pmk1p activity in growing cells and associate with, and dephosphorylate Pmk1p both in vitro and in vivo. Our results with Ptc1p provide the first biochemical evidence for a PP2C-type phosphatase acting on more than one MAPK in yeast cells. Importantly, the SAPK-dependent down-regulation of Pmk1p through Pyp1p, Pyp2p, and Ptc1p was not complete, and Pyp1p and Ptc1p phosphatases are able to negatively regulate MAPK Pmk1p activity by an alternative regulatory mechanism. Our data also indicate that Pmk1p phosphorylation oscillates as a function of the cell cycle, peaking at cell separation during cytokinesis, and that Pmp1p phosphatase plays a main role in regulating this process.
Genetic and environmental contributions to prosocial behaviour in 2- to 9-year-old South Korean twins
Authors: Hur Yoon-Mi , Rushton J. Philippe
Published: August 2007

Although over 50 twin and adoption studies have been performed on the genetic architecture of antisocial behaviour, far fewer studies have investigated prosocial behaviour, and none have done so on a non-western population. The present study examined mothers' ratings of prosocial behaviour in 514 pairs of 2- to 9-year-old South Korean monozygotic and dizygotic twins. Correlational analyses showed a tendency of increasing genetic effects and decreasing shared environmental effects with age although shared family environment effects and the moderating effects of age did not attain statistical significance in model-fitting analyses. The best-fitting model indicated that 55% (95% CI: 45–64%) of the variance in the 2- to 9-year-olds' prosocial behaviour was due to genetic factors and 45% (95% CI: 36–55%) was due to non-shared environmental factors. It is concluded that genetic and environmental influences on prosocial behaviour in young South Koreans are mostly similar to those in western samples.
Widespread endocrine disruption and reproductive impairment in an estuarine fish population exposed to seasonal hypoxia
Authors: Thomas Peter , Rahman Md. Saydur , Khan Izhar A , Kummer James A
Published: August 2007

The long-term effects on marine fish populations of the recent increase worldwide in the incidence of coastal hypoxia are unknown. Here we show that chronic environmental exposure of Atlantic croaker (Micropogonias undulatus) to hypoxia in a Florida estuary caused marked suppression of ovarian and testicular growth which was accompanied by endocrine disruption. Laboratory hypoxia studies showed that the endocrine disruption was associated with impairment of reproductive neuroendocrine function and decreases in hypothalamic serotonin (5-HT) content and the activity of the 5-HT biosynthetic enzyme, tryptophan hydroxylase. Pharmacological restoration of hypothalamic 5-HT levels also restored neuroendocrine function, indicating that the stimulatory serotonergic neuroendocrine pathway is a major site of hypoxia-induced inhibition. Inhibition of tryptophan hydroxylase activity to downregulate reproductive activity could have evolved as an adaptive mechanism to survive periodic hypoxia, but in view of the recent increased incidence of coastal hypoxia could become maladaptive and potentially affect fish population abundance and threaten valuable fishery resources.
Breeding for abiotic stresses for sustainable agriculture
Authors: Witcombe J.R , Hollington P.A , Howarth C.J , Reader S , Steele K.A
Published: August 2007

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.
Biotic interactions, ecological knowledge and agriculture
Authors: Shennan Carol
Published: August 2007

This paper discusses biotic interactions in agroecosystems and how they may be manipulated to support crop productivity and environmental health by provision of ecosystem services such as weed, pest and disease management, nutrient cycling and biodiversity conservation. Important elements for understanding biotic interactions include consideration of the effects of diversity, species composition and food web structure on ecosystem processes; the impacts of timing, frequency and intensity of disturbance; and the importance of multitrophic interactions. All of these elements need to be considered at multiple scales that depend in part on the range of the movement of the organisms involved. These issues are first discussed in general, followed by an examination of the application of these concepts in agricultural management. The potential for a greater use of ecological management approaches is high; however, owing to the nature of complex interactions in ecosystems, there is some inherent unpredictability about responses to management interventions under different conditions. Such uncertainty needs to be accommodated in the development of recommendations for farm management. This requires an increased emphasis on the effective synthesis of complex and often apparently contradictory information and on field-based adaptive research, monitoring and social learning by farmer/researcher collaborations.
Agricultural biosecurity
Authors: Waage J.K , Mumford J.D
Published: August 2007

The prevention and control of new pest and disease introductions is an agricultural challenge which is attracting growing public interest. This interest is in part driven by an impression that the threat is increasing, but there has been little analysis of the changing rates of biosecurity threat, and existing evidence is equivocal. Traditional biosecurity systems for animals and plants differ substantially but are beginning to converge. Bio-economic modelling of risk will be a valuable tool in guiding the allocation of limited resources for biosecurity. The future of prevention and management systems will be strongly influenced by new technology and the growing role of the private sector. Overall, today's biosecurity systems are challenged by changing national priorities regarding trade, by new concerns about environmental effects of biological invasions and by the question ‘who pays?’. Tomorrow's systems may need to be quite different to be effective. We suggest three changes: an integration of plant and animal biosecurity around a common, proactive, risk-based approach; a greater focus on international cooperation to deal with threats at source; and a commitment to refocus biosecurity on building resilience to invasion into agroecosystems rather than building walls around them.
The role of biotechnology for agricultural sustainability in Africa
Authors: Thomson Jennifer A
Published: August 2007

Sub-Saharan Africa could have a shortfall of nearly 90 Mt of cereals by the year 2025 if current agricultural practices are maintained. Biotechnology is one of the ways to improve agricultural production. Insect-resistant varieties of maize and cotton suitable for the subcontinent have been identified as already having a significant impact. Virus-resistant crops are under development. These include maize resistant to the African endemic maize streak virus and cassava resistant to African cassava mosaic virus. Parasitic weeds such asStrigaattack the roots of crops such as maize, millet, sorghum and upland rice. Field trials in Kenya using a variety of maize resistant to a herbicide have proven very successful. Drought-tolerant crops are also under development as are improved varieties of local African crops such as bananas, cassava, sorghum and sweet potatoes.
The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution
Authors: Chevance Fabienne F.V. , Takahashi Noriko , Karlinsey Joyce E. , Gnerer Joshua , Hirano Takanori , Samudrala Ram , Aizawa Shin-Ichi , Hughes Kelly T.
Published: August 2007

The rod component of the bacterial flagellum polymerizes from the inner membrane across the periplasmic space and stops at a length of 25 nm at the outer membrane. Bushing structures, the P- and L-rings, polymerize around the distal rod and form a pore in the outer membrane. The flagellar hook structure is then added to the distal rod growing outside the cell. Hook polymerization stops after the rod–hook structure reaches ∼80 nm in length. This study describes mutants in the distal rod protein FlgG that fail to terminate rod growth. The mutant FlgG subunits continue to polymerize close to the length of the normal rod–hook structure of 80 nm. These filamentous rod structures have multiple P-rings and fail to form the L-ring pore at the outer membrane. The flagella grow within the periplasm similar to spirochete flagella. This provides a simple method to evolve intracellular flagella as in spirochetes. The mechanism that couples rod growth termination to the ring assembly and outer membrane penetration exemplifies the importance of stopping points in the construction of a complex macromolecular machine that facilitate efficient coupling to the next step in the assembly pathway.
Control of appetitive and aversive taste-reactivity responses by an auditory conditioned stimulus in a devaluation task: A FOS and behavioral analysis
Authors: Kerfoot Erin C. , Agarwal Isha , Lee Hongjoo J. , Holland Peter C.
Published: August 2007

Through associative learning, cues for biologically significant reinforcers such as food may gain access to mental representations of those reinforcers. Here, we used devaluation procedures, behavioral assessment of hedonic taste-reactivity responses, and measurement of immediate-early gene (IEG) expression to show that a cue for food engages behavior and brain activity related to sensory and hedonic processing of that food. Rats first received a tone paired with intraoral infusion of sucrose. Then, in the absence of the tone, the value of sucrose was reduced (Devalue group) by pairing sucrose with lithium chloride (LiCl), or maintained (Maintain group) by presenting sucrose and LiCl unpaired. Finally, taste-reactivity responses to the tone were assessed in the absence of sucrose. Devalue rats showed high levels of aversive responses and minimal appetitive responses, whereas Maintain rats exhibited substantial appetitive responding but little aversive responding. Control rats that had not received tone–sucrose pairings did not display either class of behaviors. Devalue rats showed greater FOS expression than Maintain rats in several brain regions implicated in devaluation task performance and the display of aversive responses, including the basolateral amygdala, orbitofrontal cortex, gustatory cortex (GC), and the posterior accumbens shell (ACBs), whereas the opposite pattern was found in the anterior ACBs. Both Devalue and Maintain rats showed greater FOS expression than control rats in amygdala central nucleus, GC, and both subregions of ACBs. Thus, through associative learning, auditory cues for food gained access to neural processing in several brain regions importantly involved in the processing of taste memory information.
Transgenic mice expressing an inhibitory truncated form of p300 exhibit long-term memory deficits
Authors: Oliveira Ana M.M. , Wood Marcelo A. , McDonough Conor B. , Abel Ted
Published: August 2007

The formation of many forms of long-term memory requires several molecular mechanisms including regulation of gene expression. The mechanisms directing transcription require not only activation of individual transcription factors but also recruitment of transcriptional coactivators. CBP and p300 are transcriptional coactivators that interact with a large number of transcription factors and regulate transcription through multiple mechanisms, including an intrinsic histone acetyltransferase (HAT) activity. HAT activity mediates acetylation of lysine residues on the amino-terminal tails of histone proteins, thereby increasing DNA accessibility for transcription factors to activate gene expression. CBP has been shown to play an important role in long-term memory formation. We have investigated whether p300 is also required for certain forms of memory. p300 shares a high degree of homology with CBP and has been shown to interact with transcription factors known to be critical for long-term memory formation. Here we demonstrate that conditional transgenic mice expressing an inhibitory truncated form of p300 (p300Δ1), which lacks the carboxy-terminal HAT and activation domains, have impaired long-term recognition memory and contextual fear memory. Thus, our study demonstrates that p300 is required for certain forms of memory and that the HAT and carboxy-terminal domains play a critical role.
Adult visual experience promotes recovery of primary visual cortex from long-term monocular deprivation
Authors: Fischer Quentin S. , Aleem Salman , Zhou Hongyi , Pham Tony A.
Published: August 2007

Prolonged visual deprivation from early childhood to maturity is believed to cause permanent visual impairment. However, there have been case reports of substantial improvement of binocular vision in human adults following lifelong visual impairment or deprivation. These observations, together with recent findings of adult ocular dominance plasticity in rodents, led us to re-examine whether adult primary visual cortex (V1) is capable of any recovery following long-term monocular deprivation starting in development. Using mice as a model, we find that monocular deprivation from early development to mature ages (well past the critical period) severely impaired binocular vision by reducing the amplitude of responses elicited by stimulation of the deprived eye. Surprisingly, we find little effect on nondeprived eye responses. Restoration of binocular vision in mature adults yields modest but significant improvement of visual responses in V1. Remarkably, we find that when binocular vision is followed by occlusion of the nondeprived eye, visual responses in V1 recover almost fully, as measured by visual evoked potential amplitude, spatial frequency threshold, and single-unit activity. We conclude that adult V1 can recover from long-term deprivation when provided with an optimal regimen of visual experience.
Solution structure of Ca2+‐free rat β‐parvalbumin (oncomodulin)
Authors: Henzl Michael T. , Tanner John J.
Published: August 2007

Relative to other parvalbumin isoforms, the mammalian β‐parvalbumin (oncomodulin) displays attenuated divalent ion affinity. High‐resolution structural data for the Ca2+‐bound protein have provided little insight into the physical basis for this behavior, prompting an examination of the unliganded state. This article describes the solution structure and peptide backbone dynamics of Ca2+‐free rat β‐parvalbumin (β‐PV). Ca2+removal evidently provokes significant structural alterations. Interaction between the D helix and the AB domain in the Ca2+‐bound protein is greatly diminished in the apo‐form, permitting the D helix to straighten. There is also a significant reorganization of the hydrophobic core and a concomitant remodeling of the interface between the AB and CD‐EF domains. These modifications perturb the orientation of the C and D helices, and the energetic penalty associated with their reversal could contribute to the low‐affinity signature of the CD site. By contrast, Ca2+removal causes a comparatively minor perturbation of the E and F helices, consistent with the more typical divalent ion affinity observed for the EF site. Ca2+‐free rat β‐PV retains structural rigidity on the picosecond–nanosecond timescale. At 20°C, the majority of amide vectors show no evidence for motion on timescales above 20 ps, and the average order parameter for the entire molecule is 0.92.
Amino‐acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: Insights from the quasi‐chemical approximation
Authors: Goldstein Richard A.
Published: August 2007

We investigate the mechanisms used by proteins to maintain thermostability throughout a wide range of temperatures. We use the quasi‐chemical approximation to estimate interaction strengths for psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Our results highlight the importance of core packing in thermophilic stability. Although we observed an increase in the number of charged residues, the contribution of salt bridges appears to be relatively modest by comparison. We observed results consistent with a gradual loosening of structure in psychrophiles, including a weakening of almost all types of interactions.