bluuebunny/crossref_metadata_2025 huggingface dataset:
Bridging Kohn - Sham DFT and the Angular Overlap Model. Ligand-Field Parameters and Bond Covalencies in Tetrahedral Complexes
Authors: Schäffer Claus E. , Anthon Christian , Bendix Jesper
Published: October 2009

Kohn–Sham density functional theory (DFT), constrained by the average-of-configuration computations, allows the valence shell of regular tetrahedral chlorido complexes of a complete series of 3d transition metal ions to be orbitally compared. The concept of classificational parentage provides a handle on the discussion of the energetic ordering of all the valence orbitals and illuminates an almost identical ordering for all the systems. Only the participation of the metal 4s orbital in bonding causes a few minor fluctuations. The partially filled ‘3d’ molecular orbitals sit in an energy window framed by completely filled ‘ligand orbitals’ on the low-energy side and an empty metal ‘4s’ orbital on the high-energy side. Regular tetrahedral symmetry requires the halides to be linearly ligating and this property is stable within the ‘experimental’ uncertainty for small distortions. By lowering the symmetry towards the planar configuration, keeping the equivalence of the ligands stable, the information content of the computations was doubled and the angular overlap energy parameters referring to the individual ligands obtained. The orbital energies of the partially filled shell depend linearly on the Angular Overlap Model (AOM) parameters eλ, the slope being the sum of the squares of the single-ligand λ angular overlaps (λ = σ and π). Mulliken population analysis shows the contents of the appropriate ligand orbitals in the ‘d’ orbitals to vary in parallel with the molecular orbital AOM energies and to increase pronouncedly with the oxidation number z. Results for tetraoxidoferrate(vi) show a remarkable resemblance with the chloride complexes of even the divalent metal ions. However, although the bonding orbitals are more π-bonding, the totally symmetrical bonding orbitals use M_4s less in the oxido complex. The sensitivity of covalency and spectroscopic energy parameters towards radial distortions are examined and show Werner-type complexes and the high-valent FeO42– to behave somewhat differently.
Seasonal changes in pasture quality and diet selection and their relationship with liveweight gain of steers grazing tropical grass and grass - legume pastures in northern Australia
Authors: Hill J. O. , Coates D. B. , Whitbread A. M. , Clem R. L. , Robertson M. J. , Pengelly B. C.
Published: October 2009

The variation in liveweight gain in grazing beef cattle as influenced by pasture type, season and year effects has important economic implications for mixed crop–livestock systems and the ability to better predict such variation would benefit beef producers by providing a guide for decision making. To identify key determinants of liveweight change of Brahman-cross steers grazing subtropical pastures, measurements of pasture quality and quantity, and diet quality in parallel with liveweight were made over two consecutive grazing seasons (48 and 46 weeks, respectively), on mixed Clitoria ternatea/grass, Stylosanthes seabrana/grass and grass swards (grass being a mixture of Bothriochloa insculpta cv. Bisset, Dichanthium sericeum and Panicum maximum var. trichoglume cv. Petrie). Steers grazing the legume-based pastures had the highest growth rate and gained between 64 and 142 kg more than those grazing the grass pastures in under 12 months. Using an exponential model, green leaf mass, green leaf %, adjusted green leaf % (adjusted for inedible woody legume stems), faecal near infrared reflectance spectroscopy predictions of diet crude protein and diet dry matter digestibility, accounted for 77, 74, 80, 63 and 60%, respectively, of the variation in daily weight gain when data were pooled across pasture types and grazing seasons. The standard error of the regressions indicated that 95% prediction intervals were large (±0.42–0.64 kg/head.day) suggesting that derived regression relationships have limited practical application for accurately estimating growth rate. In this study, animal factors, especially compensatory growth effects, appeared to have a major influence on growth rate in relation to pasture and diet attributes. It was concluded that predictions of growth rate based only on pasture or diet attributes are unlikely to be accurate or reliable. Nevertheless, key pasture attributes such as green leaf mass and green leaf % provide a robust indication of what proportion of the potential growth rate of the grazing animals can be achieved.
Effects of increasing the inclusion level of Atriplex amnicola in the diet of sheep
Authors: Mahipala M. B. P. Kumara , Krebs G. L. , McCafferty P. , Dods K.
Published: October 2009

The effects of increasing the level of inclusion of fresh Atriplex amnicola Paul G.Wilson foliage in an oaten chaff (Avena sativa L.) diet fed to sheep were investigated. Six experimental diets were formulated to contain varying amounts [0, 161, 362, 496, 650 and 836 g/kg diet dry matter (DM)] of A. amnicola, and these diets were fed to individually penned sheep according to a Latin square design. Feed and faecal samples were analysed for crude protein, neutral detergent fibre, acid detergent fibre, acid detergent lignin, and ash contents. Mineral contents and 24 h in vitro gas production were measured in freeze-dried feed samples. As the level of inclusion of A. amnicola increased, digestibility of DM, organic matter and neutral detergent fibre increased (P < 0.05), reaching the peak at the 496 g/kg DM inclusion level and then decreasing (P < 0.05) thereafter. Acid detergent fibre digestibility followed a similar trend, but peak digestibility was at 362 g/kg DM inclusion level. Digestibility of crude protein continued to increase (P < 0.05) with increasing inclusion of A. amnicola. Gas production (24 h) from A. amnicola was lower (P < 0.05) than that from oaten chaff (24.4 v. 45.3 mL/200 mg DM) and also had lower metabolisable energy content (in vitro ME, 6.3 v. 8.6 MJ/kg DM). As the level of inclusion of A. amnicola in the diet increased, gas production and in vitro metabolisable energy content decreased (P < 0.05). The 496 g/kg DM inclusion level provided the optimum N : energy ratio for fermentation of dietary fibre. At this level of inclusion the diet was rich in Na, Ca, P, Mg, K, S, Mn and Zn. High inclusion levels improved the crude protein value of the diet but compromised fibre digestibility.
Niches, models, and climate change: Assessing the assumptions and uncertainties
Authors: Wiens John A. , Stralberg Diana , Jongsomjit Dennis , Howell Christine A. , Snyder Mark A.
Published: October 2009

As the rate and magnitude of climate change accelerate, understanding the consequences becomes increasingly important. Species distribution models (SDMs) based on current ecological niche constraints are used to project future species distributions. These models contain assumptions that add to the uncertainty in model projections stemming from the structure of the models, the algorithms used to translate niche associations into distributional probabilities, the quality and quantity of data, and mismatches between the scales of modeling and data. We illustrate the application of SDMs using two climate models and two distributional algorithms, together with information on distributional shifts in vegetation types, to project fine-scale future distributions of 60 California landbird species. Most species are projected to decrease in distribution by 2070. Changes in total species richness vary over the state, with large losses of species in some “hotspots” of vulnerability. Differences in distributional shifts among species will change species co-occurrences, creating spatial variation in similarities between current and future assemblages. We use these analyses to consider how assumptions can be addressed and uncertainties reduced. SDMs can provide a useful way to incorporate future conditions into conservation and management practices and decisions, but the uncertainties of model projections must be balanced with the risks of taking the wrong actions or the costs of inaction. Doing this will require that the sources and magnitudes of uncertainty are documented, and that conservationists and resource managers be willing to act despite the uncertainties. The alternative, of ignoring the future, is not an option.
Reducing abrupt climate change risk using the Montreal Protocol and other regulatory actions to complement cuts in CO
2
emissions
Authors: Molina Mario , Zaelke Durwood , Sarma K. Madhava , Andersen Stephen O. , Ramanathan Veerabhadran , Kaniaru Donald
Published: October 2009

Current emissions of anthropogenic greenhouse gases (GHGs) have already committed the planet to an increase in average surface temperature by the end of the century that may be above the critical threshold for tipping elements of the climate system into abrupt change with potentially irreversible and unmanageable consequences. This would mean that the climate system is close to entering if not already within the zone of “dangerous anthropogenic interference” (DAI). Scientific and policy literature refers to the need for “early,” “urgent,” “rapid,” and “fast-action” mitigation to help avoid DAI and abrupt climate changes. We define “fast-action” to include regulatory measures that can begin within 2–3 years, be substantially implemented in 5–10 years, and produce a climate response within decades. We discuss strategies for short-lived non-CO
2
GHGs and particles, where existing agreements can be used to accomplish mitigation objectives. Policy makers can amend the Montreal Protocol to phase down the production and consumption of hydrofluorocarbons (HFCs) with high global warming potential. Other fast-action strategies can reduce emissions of black carbon particles and precursor gases that lead to ozone formation in the lower atmosphere, and increase biosequestration, including through biochar. These and other fast-action strategies may reduce the risk of abrupt climate change in the next few decades by complementing cuts in CO
2
emissions.
Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state
Authors: Arunkumar Alphonse I. , Campanello Gregory C. , Giedroc David P.
Published: October 2009

Staphylococcus aureus
CzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal α5-sensing sites, some 15 Å distant from the DNA-binding interface, and allosterically inhibits DNA binding. This regulation is characterized by a large allosteric coupling free energy (Δ
G
c) of approximately +6 kcal mol
−1
, the molecular origin of which is poorly understood. Here, we report the solution quaternary structure of homodimeric CzrA bound to a palindromic 28-bp
czr
operator, a structure that provides an opportunity to compare the two allosteric “end” states of an ArsR family sensor. Zn(II) binding drives a quaternary structural switch from a “closed” DNA-binding state to a low affinity “open” conformation as a result of a dramatic change in the relative orientations of the winged helical DNA binding domains within the dimer. Zn(II) binding also effectively quenches both rapid and intermediate timescale internal motions of apo-CzrA while stabilizing the native state ensemble. In contrast, DNA binding significantly enhances protein motions in the allosteric sites and reduces the stability of the α5 helices as measured by H-D solvent exchange. This study reveals how changes in the global structure and dynamics drive a long-range allosteric response in a large subfamily of bacterial metal sensor proteins, and provides insights on how other structural classes of ArsR sensor proteins may be regulated by metal binding.
Ribosomal DNA contributes to global chromatin regulation
Authors: Paredes Silvana , Maggert Keith A.
Published: October 2009

The 35S ribosomal RNA genes (
rDNA
) are organized as repeated arrays in many organisms. Epigenetic regulation of transcription of the rRNA results in only a subset of copies being transcribed, making
rDNA
an important model for understanding epigenetic chromatin modification. We have created an allelic series of deletions within the
rDNA
array of the
Drosophila Y
chromosome that affect nucleolus size and morphology, but do not limit steady-state rRNA concentrations. These
rDNA
deletions result in reduced heterochromatin-induced gene silencing elsewhere in the genome, and the extent of the
rDNA
deletion correlates with the loss of silencing. Consistent with this, chromosomes isolated from strains mutated in genes required for proper heterochromatin formation have very small
rDNA
arrays, reinforcing the connection between heterochromatin and the
rDNA
. In wild-type cells, which undergo spontaneous natural
rDNA
loss, we observed the same correlation between loss of
rDNA
and loss of heterochromatin-induced silencing, showing that the volatility of
rDNA
arrays may epigenetically influence gene expression through normal development and differentiation. We propose that the
rDNA
contributes to a balance between heterochromatin and euchromatin in the nucleus, and alterations in
rDNA
—induced or natural—affect this balance.
A single Argonaute gene is required for induction of RNA silencing antiviral defense and promotes viral RNA recombination
Authors: Sun Qihong , Choi Gil H. , Nuss Donald L.
Published: October 2009

Dicer gene
dcl2
, required for the RNA silencing antiviral defense response in the chestnut blight fungus
Cryphonectria parasitica
, is inducible upon mycovirus infection and promotes viral RNA recombination. We now report that the antiviral defense response requires only one of the four
C. parasitica
Argonaute-like protein genes,
agl2
. The
agl2
gene is required for the virus-induced increase in
dcl2
transcript accumulation.
Agl2
and
dcl2
transcripts accumulated to much higher levels in response to hairpin RNA production or infection by a mutant CHV1-EP713 hypovirus lacking the suppressor of RNA silencing p29 than to wild-type CHV1-EP713. Similar results were obtained for an
agl2
-promoter/EGFP-reporter construct, indicating that p29-mediated repression of
agl2
transcript accumulation is promoter-dependent. Significantly, the
agl2
deletion mutant exhibited stable maintenance of non-viral sequences in recombinant hypovirus RNA virus vectors and the absence of hypovirus-defective interfering (DI) RNA production. These results establish a key role for an Argonaute gene in the induction of an RNA silencing antiviral defense response and the promotion of viral RNA recombination. They also provide evidence for a mechanism by which a virus-encoded RNA silencing suppressor represses the transcriptional induction of an RNA silencing component.
An experimental platform for systemic drug delivery to the retina
Authors: Campbell Matthew , Nguyen Anh T. H. , Kiang Anna-Sophia , Tam Lawrence C. S. , Gobbo Oliviero L. , Kerskens Christian , Dhubhghaill Sorcha Ni , Humphries Marian M. , Farrar G.-Jane , Kenna Paul F. , Humphries Peter
Published: October 2009

Degenerative retinopathies, including age-related macular degeneration, diabetic retinopathy, and hereditary retinal disorders—major causes of world blindness—are potentially treatable by using low-molecular weight neuroprotective, antiapoptotic, or antineovascular drugs. These agents are, however, not in current systemic use owing to, among other factors, their inability to passively diffuse across the microvasculature of the retina because of the presence of the inner blood–retina barrier (iBRB). Moreover, preclinical assessment of the efficacies of new formulations in the treatment of such conditions is similarly compromised. We describe here an experimental process for RNAi-mediated, size-selective, transient, and reversible modulation of the iBRB in mice to molecules up to 800 Da by suppression of transcripts encoding claudin-5, a protein component of the tight junctions of the inner retinal vasculature. MRI produced no evidence indicative of brain or retinal edema, and the process resulted in minimal disturbance of global transcriptional patterns analyzed in neuronal tissue. We show that visual function can be improved in IMPDH1
−/−
mice, a model of autosomal recessive retinitis pigmentosa, and that the rate of photoreceptor cell death can be reduced in a model of light-induced retinal degeneration by systemic drug delivery after reversible barrier opening. These findings provide a platform for high-throughput drug screening in models of retinal degeneration, and they ultimately could result in the development of a novel “humanized” approach to therapy for conditions with little or no current forms of treatment.
Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring
Authors: Smith Joel , Davidson Eric H.
Published: October 2009

Design features that ensure reproducible and invariant embryonic processes are major characteristics of current gene regulatory network models. New
cis
-regulatory studies on a gene regulatory network subcircuit activated early in the development of the sea urchin embryo reveal a sequence of encoded “fail-safe” regulatory devices. These ensure the maintenance of fate separation between skeletogenic and nonskeletogenic mesoderm lineages. An unexpected consequence of the network design revealed in the course of these experiments is that it enables the embryo to “recover” from regulatory interference that has catastrophic effects if this feature is disarmed. A reengineered regulatory system inserted into the embryo was used to prove how this system operates in vivo. Genomically encoded backup control circuitry thus provides the mechanism underlying a specific example of the regulative development for which the sea urchin embryo has long been famous.
The electrochemical approach to concerted proton—electron transfers in the oxidation of phenols in water
Authors: Costentin Cyrille , Louault Cyril , Robert Marc , Savéant Jean-Michel
Published: October 2009

Establishing mechanisms and intrinsic reactivity in the oxidation of phenol with water as the proton acceptor is a fundamental task relevant to many reactions occurring in natural systems. Thanks to the easy measure of the reaction kinetics by the current and the setting of the driving force by the electrode potential, the electrochemical approach is particularly suited to this endeavor. Despite challenging difficulties related to self-inhibition blocking the electrode surface, experimental conditions were established that allowed a reliable analysis of the thermodynamics and mechanisms of the proton-coupled electron-transfer oxidation of phenol to be carried out by means of cyclic voltammetry. The thermodynamic characterization was conducted in buffer media whereas the mechanisms were revealed in unbuffered water. Unambiguous evidence of a concerted proton–electron transfer mechanism, with water as proton acceptor, was thus gathered by simulation of the experimental data with appropriately derived theoretical relationships, leading to the determination of a remarkably large intrinsic rate constant. The same strategy also allowed the quantitative analysis of the competition between the concerted proton–electron transfer pathway and an OH
−
-triggered stepwise pathway (proton transfer followed by electron transfer) at high pHs. Investigation of the passage between unbuffered and buffered media with the example of the PO
4
H
2
−
/PO
4
H
2−
couple revealed the prevalence of a mechanism involving a proton transfer preceding an electron transfer over a PO
4
H
2−
-triggered concerted process.
Podosomes are present in a postsynaptic apparatus and participate in its maturation
Authors: Proszynski Tomasz J. , Gingras Jacinthe , Valdez Gregorio , Krzewski Konrad , Sanes Joshua R.
Published: October 2009

A critical step in synapse formation is the clustering of neurotransmitter receptors in the postsynaptic membrane, directly opposite the nerve terminal. At the neuromuscular junction, a widely studied model synapse, acetylcholine receptors (AChRs) initially aggregate to form an ovoid postsynaptic plaque. As the synapse matures, the plaque becomes perforated and is eventually transformed into a complex, branched structure. We found that this transformation also occurs in myotubes cultured in the absence of neurons, and used this system to seek machinery that orchestrates postsynaptic maturation. We show that perforations in the AChR aggregate bear structures resembling podosomes, dynamic actin-rich adhesive organelles involved in matrix remodeling in non-neuronal cells but not described in neural structures. The location and dynamics of synaptic podosomes are spatiotemporally correlated with changes in AChR aggregate topology, and pharmacological disruption of podosomes leads to rapid alterations in AChR organization. Our results indicate that synaptic podosomes play critical roles in maturation of the postsynaptic membrane.
Does teaching a solution‐focused model of counselling work? A follow‐up of graduates
Authors: Miller Judi H.
Published: October 2009

Objective: To explore the ways in which graduates of a university counsellor‐education programme reflected on their career development, retained the programme's distinctive theoretical counselling model in their counselling practice and engaged in continuing professional development. The main aim was to discover whether or not teaching a solution‐focused model of counselling was worthwhile. Method: A questionnaire, using primarily solution‐focused type questions, was distributed to all graduates. Interest was focused on specific events, both inside and outside the training programme and beyond, that contributed to graduates' sense of development as counsellors. Results: Thirty four graduates (response rate 62%) provided responses indicating their recognition that their sense of competence and identification as professional counsellors develops over time, and is assisted by relevant feedback and supervision from lecturers and practical counselling experience. Graduates also indicated that their favoured working model was solution‐focused and that, as a framework, it provided them with opportunities to integrate other counselling models and add complementary professional development education. Conclusion: The graduates' continued use of a solution‐focused model supports the view that teaching the solution‐focused model is working. The findings are considered alongside four models of counsellor development and implications for counsellor‐education programmes are explored.
Pex3 peroxisome biogenesis proteins function in peroxisome inheritance as class V myosin receptors
Authors: Chang Jinlan , Mast Fred D. , Fagarasanu Andrei , Rachubinski Dorian A. , Eitzen Gary A. , Dacks Joel B. , Rachubinski Richard A.
Published: October 2009

In Saccharomyces cerevisiae, peroxisomal inheritance from mother cell to bud is conducted by the class V myosin motor, Myo2p. However, homologues of S. cerevisiae Myo2p peroxisomal receptor, Inp2p, are not readily identifiable outside the Saccharomycetaceae family. Here, we demonstrate an unexpected role for Pex3 proteins in peroxisome inheritance. Both Pex3p and Pex3Bp are peroxisomal integral membrane proteins that function as peroxisomal receptors for class V myosin through direct interaction with the myosin globular tail. In cells lacking Pex3Bp, peroxisomes are preferentially retained by the mother cell, whereas most peroxisomes gather and are transferred en masse to the bud in cells overexpressing Pex3Bp or Pex3p. Our results reveal an unprecedented role for members of the Pex3 protein family in peroxisome motility and inheritance in addition to their well-established role in peroxisome biogenesis at the endoplasmic reticulum. Our results point to a temporal link between peroxisome formation and inheritance and delineate a general mechanism of peroxisome inheritance in eukaryotic cells.
Differential regulation of telomere and centromere cohesion by the Scc3 homologues SA1 and SA2, respectively, in human cells
Authors: Canudas Silvia , Smith Susan
Published: October 2009

Replicated sister chromatids are held together until mitosis by cohesin, a conserved multisubunit complex comprised of Smc1, Smc3, Scc1, and Scc3, which in vertebrate cells exists as two closely related homologues (SA1 and SA2). Here, we show that cohesinSA1 and cohesinSA2 are differentially required for telomere and centromere cohesion, respectively. Cells deficient in SA1 are unable to establish or maintain cohesion between sister telomeres after DNA replication in S phase. The same phenotype is observed upon depletion of the telomeric protein TIN2. In contrast, in SA2-depleted cells telomere cohesion is normal, but centromere cohesion is prematurely lost. We demonstrate that loss of telomere cohesion has dramatic consequences on chromosome morphology and function. In the absence of sister telomere cohesion, cells are unable to repair chromatid breaks and suffer sister telomere loss. Our studies elucidate the functional distinction between the Scc3 homologues in human cells and further reveal an essential role for sister telomere cohesion in genomic integrity.
Leukotriene E4–induced pulmonary inflammation is mediated by the P2Y12 receptor
Authors: Paruchuri Sailaja , Tashimo Hiroyuki , Feng Chunli , Maekawa Akiko , Xing Wei , Jiang Yongfeng , Kanaoka Yoshihide , Conley Pamela , Boyce Joshua A.
Published: October 2009

Of the potent lipid inflammatory mediators comprising the cysteinyl leukotrienes (LTs; LTC4, LTD4, and LTE4), only LTE4 is stable and abundant in vivo. Although LTE4 shows negligible activity at the type 1 and 2 receptors for cys-LTs (CysLT1R and CysLT2R), it is a powerful inducer of mucosal eosinophilia and airway hyperresponsiveness in humans with asthma. We show that the adenosine diphosphate (ADP)–reactive purinergic (P2Y12) receptor is required for LTE4-mediated pulmonary inflammation. P2Y12 receptor expression permits LTE4 -induced activation of extracellular signal-regulated kinase in Chinese hamster ovary cells and permits chemokine and prostaglandin D2 production by LAD2 cells, a human mast cell line. P2Y12 receptor expression by LAD2 cells is required for competition between radiolabeled ADP and unlabeled LTE4 but not for direct binding of LTE4, suggesting that P2Y12 complexes with another receptor to recognize LTE4. Administration of LTE4 to the airways of sensitized mice potentiates eosinophilia, goblet cell metaplasia, and expression of interleukin-13 in response to low-dose aerosolized allergen. These responses persist in mice lacking both CysLT1R and CysLT2R but not in mice lacking P2Y12 receptors. The effects of LTE4 on P2Y12 in the airway were abrogated by platelet depletion. Thus, the P2Y12 receptor is required for proinflammatory actions of the stable abundant mediator LTE4 and is a novel potential therapeutic target for asthma.
Dispersal and Movement Mechanisms of Phytophthora capsici Sporangia
Authors: Granke L. L. , Windstam S. T. , Hoch H. C. , Smart C. D. , Hausbeck M. K.
Published: October 2009

Understanding the mechanisms of Phytophthora capsici sporangial dissemination is paramount to understanding epidemic initiation and development. Direct laboratory observations showed P. capsici sporangial dispersal occurred in water with capillary force, but did not occur in response to wind or a reduction in relative humidity. Atmospheric sporangial concentrations were monitored under field conditions using a volumetric spore sampler in a commercial cucurbit field and in an experimental setting where copious sporangia were continuously available in close proximity to the spore trap. Dispersal was infrequent (0.7% of total hours monitored) during sampling in a commercial field; 14 sporangia were detected during a 7.5-week sampling period. In the experimental field situation, dispersal occurred in 4.6% of the hours sampled and 438 sporangia were impacted onto tapes during a 7-week sampling period. Airborne sporangial concentrations were positively associated with rainfall at both sites, but not vapor pressure deficit. Furthermore, in the experimental field situation, wind speed was not significant in regression analysis. Wind speed was not measured in the commercial field. Hence, both direct laboratory observations and volumetric spore sampling indicate that dispersal of sporangia via wind currents is infrequent, and sporangia are unlikely to be naturally dispersed among fields by wind alone.
APC promoter hypermethylation is an early event in endometrial tumorigenesis
Authors: Ignatov Atanas , Bischoff Joachim , Ignatov Tanja , Schwarzenau Christa , Krebs Thomas , Kuester Doerthe , Costa Serban D. , Roessner Albert , Semczuk Andrzej , Schneider‐Stock Regine
Published: October 2009

The aim of the current study was to investigate the role of promoter methylation of adenomatous polyposis coli (APC) and epithelial cadherin (E‐cadherin) genes in endometrial tumorigenesis. The methylation status of both genes was investigated in 43 cases of normal endometrium, 21 simple hyperplasia, 17 atypical hyperplasia, and 86 endometrial carcinoma (EC). Additionally, the methylation pattern of both genes was analyzed in 24 primary ECs and their corresponding metastases. DNA methylation of the APC gene increased from atypical hyperplasia (23.5%) to endometrial carcinoma, reaching its highest level of 77.4% in early stage cancer (FIGO I and II) and decreasing stepwise to 24.2% in advanced stage carcinomas (FIGO III and IV). No methylation of APC was found in normal endometrium or simple hyperplasia. Methylation of E‐cadherin was found only in EC (22.1%). The mean age of the patients with aberrant APC methylation was 68.8 years and was significantly higher compared to the mean age (60.9 years) of the patients without methylation of APC promoter (P = 0.02). APC promoter methylation significantly correlated with decreased protein expression of APC (P = 0.039), with increased expression of the Ki‐67 proliferative marker (P = 0.006) and decreased metastatic potential (P = 0.002). There was no correlation between APC and E‐cadherin methylation patterns and the other clinicopathologic features, nor with patient outcome. Our results suggest that hypermethylation of APC promoter region is an early event in endometrial tumorigenesis. (Cancer Sci 2009)
Critical roles of T‐LAK cell‐originated protein kinase in cytokinesis
Authors: Park Jae‐Hyun , Nishidate Toshihiko , Nakamura Yusuke , Katagiri Toyomasa
Published: October 2009

We previously reported up‐regulation of T‐LAK cell‐originated protein kinase (TOPK), a novel mitotic kinase, in the great majority of breast cancers. Here we report its critical roles in mitosis, especially in cytokinesis. We found that protein phosphatase 1 alpha (PP1α) inactivation by cyclin‐dependent kinase 1 (CDK1)/cyclin B1 caused enhancement of autophosphorylation of TOPK and resulted in its activation at an early stage of mitosis. Then TOPK interacted with and phosphorylated p97, a member of the AAA+ family of ATPase proteins, through an interaction with p47 protein as an adaptor protein. Interestingly, knockdown of TOPK or p97 in breast cancer cells caused the mitotic failures in the abscission process. This mitotic failure could be rescued by additional exogenous introduction of wild‐type TOPK protein, but not by that of its kinase‐dead form. Our findings suggest that TOPK is indispensable for cancer cell cytokinesis throughout phosphorylation on p97. (Cancer Sci 2009)
Does designation of protected areas ensure conservation of tree diversity in the Sudanian dry forest of Burkina Faso?
Authors: Paré Souleymane , Tigabu Mulualem , Savadogo Patrice , Odén Per Christer , Ouadba Jean Marie
Published: October 2009

The importance of conservation status of the forest (protected versus unprotected) at two sites with differing human population density (high versus low) on the tree diversity of a Sudanian dry forest in Burkina Faso was studied. All woody species were recorded in 127 circular plots (area = 456.16 m2), and density, dominance, frequency, importance value indices and a variety of diversity measures were calculated to assess the species composition, structure and heterogeneity. A total of 69 species, representing 26 families and 52 genera, were found. Combretaceae, Leguminosae subfamily Caesalpinioideae and Rubiaceae were the dominant families. Neither human pressure nor forest conservation status significantly influenced the tree species richness. Stem density and basal area were significantly higher at the site with high population density than otherwise. Fisher’s diversity index revealed the unprotected forest at the site with low population density as the most diverse. We identified species with high conservation importance that should be enriched to maintain a viable population size. In conclusion, the current designation of protected areas seems inefficient at ensuring the conservation of tree diversity in the forest reserve. Thus, participatory conservation programme should be initiated.
The increasing hospital disease burden of haemochromatosis in England
Authors: COWAN M. L. , WESTLAKE S. , THOMSON S. J. , RAHMAN T. M. , MAJEED A. , MAXWELL J. D. , KANG J.‐Y.
Published: October 2009

Background  Hereditary haemochromatosis is a preventable cause of liver disease with an increasing disease burden.

Aims  To investigate time trends for hospital admission ascribed to haemochromatosis in England during the period from 1989/1990 to 2002/2003 and mortality from 1979 to 2005.

Methods  Hospital admission data, relating to both in‐patients and day‐cases, were obtained from the Hospital Episodes Statistics service. Mortality rates for England and Wales were provided by the Office for National Statistics.

Results  Haemochromatosis is an uncommon cause for hospital admission. Age‐standardized in‐patient admission rates increased over the study period by 269% in men and by 290% in women: (from 0.64 to 2.36 and from 0.21 to 0.81 per year per 100 000). The increase in age‐standardized day‐case admission rates was even higher (men: from 2.78 to 34.9 per year per 100 000, 1155%; women: from 0.58 to 11.67 per year per 100 000, 1924%). Haemochromatosis was recorded as an uncommon cause of death.

Conclusions  Hospital in‐patient and day case admissions for haemochromatosis increased markedly over the study period while mortality remained low. Both admission rates and mortality were higher in men than in women. The increase in admission rate may reflect improved recognition and diagnosis of iron overload disorders following identification of the HFE gene.

Aliment Pharmacol Ther 31, 247–252
Incidence and reasons for late failure after allogeneic haematopoietic cell transplantation following BuCy2 in acute myeloid leukaemia
Authors: Pant Shubham , Hamadani Mehdi , Dodds Anthony J. , Szer Jeffrey , Crilley Pamela A. , Stevenson Dustin , Phillips Gary , Elder Patrick , Nivison‐Smith Ian , Avalos Belinda R. , Penza Sam , Topolsky David , Sobecks Ronald , Kalaycio Matt , Bolwell Brian J. , Copelan Edward A.
Published: October 2009

The long‐term follow‐up is presented for 317 patients with acute myeloid leukaemia who underwent human leucocyte antigen‐identical sibling marrow transplants between 1984 and 1995 following preparation with busulfan 16 mg/kg and cyclophosphamide 120 mg/kg. Among the 142 (45%) who were alive and leukaemia‐free 3 years following transplantation, the leukaemia‐free survival at 15 years was 72·8%. The cumulative incidence of late (>3 years beyond transplant) non‐relapse mortality at 15 years was 12·9% and of late relapse was 16·5%. None of the variables considered (including age, disease stage, and graft‐versus‐host disease) were predictive of late failure.
Long-term T cell memory to human leucocyte antigen-A2 supertype epitopes in humans vaccinated against smallpox
Authors: Ostrout N D , McHugh M M , Tisch D J , Moormann A M , Brusic V , Kazura J W
Published: October 2009

Identification of human leucocyte antigen (HLA) class I-restricted T cell epitopes is important to develop methods to track the evolution of T cell memory to new generation smallpox vaccines and allow comparison to older vaccinia virus preparations known to induce protection against smallpox. We evaluated the relative predictive values of four computational algorithms to identify candidate 9-mer HLA-A2 supertype epitopes that were confirmed to stimulate preferentially T cell interferon (IFN)-γ responses by subjects last vaccinated with Dryvax 27–54 years previously. Six peptides encoded by I4L, G1L, A8R, I8R, D12L and H3L open reading frames that were identical for Vaccinia (Copenhagen), Variola major (Bangledesh 1975) and modified vaccinia Ankara strain preferentially stimulated IFN-γ responses by healthy HLA-A2 supertype adults last given Dryvax 27–49 years earlier relative to remotely vaccinated non-HLA-A2 supertype and unvaccinated HLA-A2 supertype adults. Combining results from at least two computational algorithms that use different strategies to predict peptide binding to HLA-A2 supertype molecules was optimal for selection of candidate peptides that were confirmed to be epitopes by recall of T cell IFN-γ responses. These data will facilitate evaluation of the immunogenicity of replication incompetent smallpox vaccines such as modified vaccinia Ankara and contribute to knowledge of poxvirus epitopes that are associated with long-lived T cell memory.
CD8+ T cell activation and differentiation in allergic asthma and the impact of cytomegalovirus serological status
Authors: Bratke K , Krieghoff L , Kuepper M , Luttmann W , Virchow J C
Published: October 2009

Allergic asthma is a chronic inflammatory T helper 2 (Th2)-associated disease. There is evidence that the atopic milieu affects the development of CD8+ T cells in patients. We therefore analysed activation and differentiation states of CD8+ T cells in asymptomatic patients regarding the cytomegalovirus serological status. Memory CD8+ T cells (CCR5highCD3+CD8+), memory/effector cells (CD27+CD28–CD3+CD8+), effector cells (CD27–CD28–CD3+CD8+) and activated CD8+ T cells (CD11b+CD3+CD8+) were identified by flow cytometry in peripheral blood of 19 (seven cytomegalovirus (CMV)+/12 CMV–) patients with allergic asthma (AA) and 21 (seven CMV+/14 CMV–) healthy controls (HC). Effector and activated CD8+ T cells were significantly elevated in CMV+ HC compared to CMV– HC. There was a non-significant trend for reduced percentages of effector CD8+ T cells in CMV+ AA (median: 10·4%, range: 4·4–33·8%) compared to CMV+ HC (median: 23·1%, range: 10·7–54·1%; P = 0·128) and in CMV– AA (median: 4·1%, range: 0·6–13·4%) compared to CMV– HC (median: 5·7%, range: 0·2–17·0%; P = 0·085). Activated CD8+ T cells were reduced significantly in CMV+ AA (median: 17·0%, range: 6·0–29·4%) compared to CMV+ HC (median: 40·4%, range: 18·9–67·0%; P = 0·004) and showed a non-significant trend in CMV– AA (median: 15·0%, range: 2·9–24·0%) compared to CMV– HC (median: 20·2%, range: 5·8–71·0%; P = 0·060). Activated CD8+ T cells are significantly reduced in CMV+ patients with allergic asthma. Furthermore, a trend for an impaired terminal CD8+ T cell differentiation is observed in CMV+ and CMV– patients with asthma.
Optimal assessment of the ability of children with recurrent respiratory tract infections to produce anti-polysaccharide antibodies
Authors: Tuerlinckx D , Vermeulen F , Pékus V , De Bilderling G , Glupczynski Y , Collet S , Jamart J , Bodart E , Mascart F
Published: October 2009

Specific anti-polysaccharide antibody deficiency (SPAD) is an immune disorder. Diagnostic criteria have not yet been defined clearly. One hundred and seventy-six children evaluated for recurrent respiratory tract infections were analysed retrospectively. For each subject, specific anti-pneumococcal antibodies had been measured with two enzyme-linked immunosorbent assays (ELISAs), one overall assay (OA) using the 23-valent pneumococcal polysaccharide vaccine (23-PPSV) as detecting antigen and the other purified pneumococcal polysaccharide serotypes (serotype-specific assay, SSA) (serotypes 14, 19F and 23F). Antibody levels were measured before (n = 176) and after (n = 93) immunization with the 23-PPSV. Before immunization, low titres were found for 138 of 176 patients (78%) with OA, compared to 20 of 176 patients (11%) with the SSA. We found a significant correlation between OA and SSA results. After immunization, 88% (71 of 81) of the patients considered as responders in the OA test were also responders in the SSA; 93% (71 of 76) of the patients classified as responders according to the SSA were also responders in the OA. SPAD was diagnosed in 8% (seven of 93) of patients on the basis of the absence of response in both tests. Thus, we propose to use OA as a screening test for SPAD before 23-PPSV immunization. After immunization, SSA should be used only in case of a low response in OA. Only the absence of or a very low antibody response detected by both tests should be used as a diagnostic criterion for SPAD.
Outcome of influenza vaccination in combat-related post-traumatic stress disorder (PTSD) patients
Authors: Kosor Krnic E , Gagro A , Kozaric-Kovacic D , Vilibic M , Grubisic-Ilic M , Folnegovic-Smalc V , Drazenovic V , Cecuk-Jelicic E , Gjenero-Margan I , Kuzman I , Jeren T , Sabioncello A , Kerhin-Brkljacic V , Kaic B , Markotic A , Gotovac K , Rabatic S , Mlinaric-Galinovic G , Dekaris D
Published: October 2009

Post-traumatic stress disorder (PTSD) is an anxiety disorder that can occur after exposure to extreme traumatic experience such as war trauma, and is accompanied by fear, helplessness or horror. Exposure to trauma can result in immune dysregulation and influence susceptibility to infectious disease as well as vaccine efficacy. The aim of the study was to determine the relation of psychological stress and the immune response to influenza vaccination in combat-related PTSD patients (n = 28). Detection of anti-viral antibody titre was performed by inhibition of haemagglutination assay. Ex vivo tetramer staining of CD8+ T lymphocytes was used to monitor T cells specific for human leucocyte antigen (HLA)-A*0201-restricted influenza A haemagglutinin antigens before and after vaccination. Twenty patients showed a fourfold antibody titre increase to one or both influenza A viral strains, and 18 of them showed the same response for both influenza B viral strains. Ten of 15 healthy controls showed a fourfold rise in antibody titre to both influenza A viral strains and eight of them showed the same response for both influenza B viral strains. HLA-A*0201+ PTSD patients (n = 10) showed a significant increase of influenza-specific CD8 T cells after vaccination. Although those PTSD patients had a lower number of influenza-specific CD8+ T cells before vaccination compared to HLA-A*0201+ healthy controls (n = 6), there was no difference in influenza A antibody titre between PTSD patients and control subjects before vaccination. The generated humoral and cellular immune response in PTSD patients argues against the hypothesis that combat-related PTSD in war veterans might affect protection following influenza vaccination.
CXCL9 and 11 in patients with pulmonary sarcoidosis: a role of alveolar macrophages
Authors: Nishioka Y , Manabe K , Kishi J , Wang W , Inayama M , Azuma M , Sone S
Published: October 2009

Interferon-inducible protein-10 (IP-10)/CXCL10, which is a ligand for CXC chemokine receptor 3 (CXCR3), is known to be involved in the pathogenesis of pulmonary sarcoidosis. However, the roles of monokine induced by interferon γ (Mig)/CXCL9 and interferon-inducible T cell α chemoattractant (I-TAC)/CXCL11, which are also CXCR3 ligands, remain unclear. Mig/CXCL9, IP-10/CXCL10 and I-TAC/CXCL11 in both bronchoalveolar lavage fluid (BALF) and serum in patients with pulmonary sarcoidosis were measured by enzyme-linked immunosorbent assay (ELISA). The expression of these chemokines in alveolar macrophages was examined using ELISA, quantitative real-time polymerase chain reaction and immunostaining. In BALF, Mig/CXCL9 and IP-10/CXCL10 were significantly elevated in stage II sarcoidosis as compared with the levels in healthy volunteers. In serum, Mig/CXCL9 and I-TAC/CXCL11 were increased in stage II of the disease. The levels of all CXCR3 ligands in BALF were correlated with the numbers of both total and CD4+ lymphocytes. Alveolar macrophages were stained positive for all CXCR3 ligands and produced increased amounts of these chemokines. Positive staining of the three chemokines was also observed in the epithelioid and giant cells in the sarcoid lungs. These findings suggest that Mig/CXCL9 and I-TAC/CXCL11 as well as IP-10/CXCL10 play important roles in the accumulation of Th1 lymphocytes in sarcoid lungs.
THIS ARTICLE HAS BEEN RETRACTED Interleukin-13-induced type II polarization of inflammatory macrophages is mediated through suppression of nuclear factor-κB and preservation of IκBα in a T cell lymphoma
Authors: Deepak P , Kumar S , Acharya A
Published: October 2009

Retraction

The article from Clinical & Experimental Immunology, ‘Interleukin-13-induced type II polarization of inflammatory macrophages is mediated through suppression of nuclear factor-κB and preservation of IκBα in a T cell lymphoma’, by P. Deepak, S. Kumar and A. Acharya (August 2007, 149(2), 378–386), published online on 5th June 2007] on Wiley InterScience (http://www.interscience.wiley.com), has been retracted by agreement between the Editor-in-Chief of Clinical & Experimental Immunology and Wiley-Blackwell.

The retraction has been agreed due to lack of original data.
Effects of an indigenous and a commercial Lactobacillus buchneri strain on quality of sugar cane silage
Authors: Ávila C. L. S. , Pinto J. C. , Figueiredo H. C. P. , Schwan R. F.
Published: October 2009

The aim was to evaluate the effects of adding a novel Lactobacillus buchneri strain and a commercial inoculant on the fermentation and aerobic stability of sugar cane silages (Saccharum spp.). In the first experiment samples were collected from sugar cane silage at 5, 20, 40 and 80 d after ensilage in experimental silos and microorganisms belonging to the Lactobacillus genus were isolated and identified, with a wild strain of L. buchneri, UFLA SIL 72, being selected as an inoculant. In the second experiment sugar cane was inoculated with either the novel bacteria or a commercial inoculant at the moment of ensiling and compared with a control silage prepared without an inoculant. Experimental silos were opened at 0, 3, 10, 30, 60 and 90 d of ensilage and their chemical composition measured. The silages opened after 90 d were also assessed for aerobic stability. The addition of L. buchneri resulted in a higher concentration of acetic acid and reduced populations of yeasts in silage compared to the other silage treatments, and a lower ethanol concentration in the silage. The novel L. buchneri isolate and the commercial inoculant also improved aerobic stability of the sugar cane silages. It was concluded that the addition of the novel inoculants L. buchneri UFLA SIL 72 to sugar cane silage can be recommended.