bluuebunny/crossref_metadata_2025 huggingface dataset:
A point mutation in the murine Hem1 gene reveals an essential role for Hematopoietic Protein 1 in lymphopoiesis and innate immunity
Authors: Park Heon , Staehling-Hampton Karen , Appleby Mark W. , Brunkow Mary E. , Habib Tania , Zhang Yi , Ramsdell Fred , Liggitt H. Denny , Freie Brian , Tsang Mark , Carlson George , Friend Sherree , Frevert Charles , Iritani Brian M.
Published: November 2008

Hem1 (Hematopoietic protein 1) is a hematopoietic cell-specific member of the Hem family of cytoplasmic adaptor proteins. Orthologues of Hem1 in Dictyostelium discoideum, Drosophila melanogaster, and Caenorhabditis elegans are essential for cytoskeletal reorganization, embryonic cell migration, and morphogenesis. However, the in vivo functions of mammalian Hem1 are not known. Using a chemical mutagenesis strategy in mice to identify novel genes involved in immune cell functions, we positionally cloned a nonsense mutation in the Hem1 gene. Hem1 deficiency results in defective F-actin polymerization and actin capping in lymphocytes and neutrophils caused by loss of the Rac-controlled actin-regulatory WAVE protein complex. T cell development is disrupted in Hem1-deficient mice at the CD4−CD8− (double negative) to CD4+CD8+ (double positive) cell stages, whereas T cell activation and adhesion are impaired. Hem1-deficient neutrophils fail to migrate in response to chemotactic agents and are deficient in their ability to phagocytose bacteria. Remarkably, some Rac-dependent functions, such as Th1 differentiation and nuclear factor κB (NF-κB)–dependent transcription of proinflammatory cytokines proceed normally in Hem1-deficient mice, whereas the production of Th17 cells are enhanced. These results demonstrate that Hem1 is essential for hematopoietic cell development, function, and homeostasis by controlling a distinct pathway leading to cytoskeletal reorganization, whereas NF-κB–dependent transcription proceeds independently of Hem1 and F-actin polymerization.
VE-PTP maintains the endothelial barrier via plakoglobin and becomes dissociated from VE-cadherin by leukocytes and by VEGF
Authors: Nottebaum Astrid F. , Cagna Giuseppe , Winderlich Mark , Gamp Alexander C. , Linnepe Ruth , Polaschegg Christian , Filippova Kristina , Lyck Ruth , Engelhardt Britta , Kamenyeva Olena , Bixel Maria Gabriele , Butz Stefan , Vestweber Dietmar
Published: November 2008

We have shown recently that vascular endothelial protein tyrosine phosphatase (VE-PTP), an endothelial-specific membrane protein, associates with vascular endothelial (VE)–cadherin and enhances VE-cadherin function in transfected cells (Nawroth, R., G. Poell, A. Ranft, U. Samulowitz, G. Fachinger, M. Golding, D.T. Shima, U. Deutsch, and D. Vestweber. 2002. EMBO J. 21:4885–4895). We show that VE-PTP is indeed required for endothelial cell contact integrity, because down-regulation of its expression enhanced endothelial cell permeability, augmented leukocyte transmigration, and inhibited VE-cadherin–mediated adhesion. Binding of neutrophils as well as lymphocytes to endothelial cells triggered rapid (5 min) dissociation of VE-PTP from VE-cadherin. This dissociation was only seen with tumor necrosis factor α–activated, but not resting, endothelial cells. Besides leukocytes, vascular endothelial growth factor also rapidly dissociated VE-PTP from VE-cadherin, indicative of a more general role of VE-PTP in the regulation of endothelial cell contacts. Dissociation of VE-PTP and VE-cadherin in endothelial cells was accompanied by tyrosine phoshorylation of VE-cadherin, β-catenin, and plakoglobin. Surprisingly, only plakoglobin but not β-catenin was necessary for VE-PTP to support VE-cadherin adhesion in endothelial cells. In addition, inhibiting the expression of VE-PTP preferentially increased tyrosine phosphorylation of plakoglobin but not β-catenin. In conclusion, leukocytes interacting with endothelial cells rapidly dissociate VE-PTP from VE-cadherin, weakening endothelial cell contacts via a mechanism that requires plakoglobin but not β-catenin.
Out of breath: GM-CSFRα mutations disrupt surfactant homeostasis
Authors: Notarangelo Luigi D. , Pessach Itai
Published: November 2008

Pulmonary alveolar proteinosis (PAP) is a rare disorder in which surfactant homeostasis in the lung is impaired, causing respiratory distress and, in severe cases, respiratory failure. Most cases of PAP are associated with the formation of autoantibodies against the cytokine granulocyte/macrophage colony-stimulating factor (GM-CSF), which is required for normal surfactant homeostasis and lung function. New studies now identify three patients in whom PAP was caused by mutations in the gene encoding the ligand-binding α chain of the GM-CSF receptor.
An update on the big bang nucleosynthesis prediction for
7Li: the problem worsens
Authors: Cyburt Richard H , Fields Brian D , Olive Keith A
Published: November 2008

The lithium problem arises from the significant discrepancy between the primordial
7Li
abundance as predicted by big bang nucleosynthesis (BBN) theory and the Wilkinson
Microwave Anisotropy Probe (WMAP) baryon density, and the pre-Galactic lithium
abundance inferred from observations of metal-poor (Population II) stars. This problem has
loomed for the past decade, with a persistent discrepancy of a factor of 2–3 in
7Li/H. Recent developments have sharpened all aspects of the Li problem. Namely: (1) BBN theory
predictions have sharpened due to new nuclear data; in particular, the uncertainty on the reaction rate
for3He(α,γ)7Be
has reduced to 7.4%, nearly a factor of 2 tighter than previous determinations.
(2) The WMAP five-year data set now yields a cosmic baryon density
with an uncertainty reduced to 2.7%. (3) Observations of metal-poor stars
have tested for systematic effects. With these, we now find that the
BBN+WMAP
predicts7Li/H = (5.24−0.67
+0.71) × 10−10. The central value represents an increase by 23%, most of which is due to the upward shift in the3He(α,γ)7Be
rate. More significant is the reduction in the7Li/H uncertainty by almost
a factor of 2, tracking
the reduction in the3He(α,γ)7Be
error bar. These changes exacerbate the Li problem; the discrepancy is now a factor 2.4 or
4.2σ (from globular
cluster stars) to 4.3 or 5.3σ
(from halo field stars). Possible resolutions to the lithium problem are briefly reviewed, and
key experimental and astronomical measurements highlighted.
Power enhancement via multivariate outlier testing with gene expression arrays
Authors: Asare Adam L. , Gao Zhong , Carey Vincent J. , Wang Richard , Seyfert-Margolis Vicki
Published: November 2008

Motivation: As the use of microarrays in human studies continues to increase, stringent quality assurance is necessary to ensure accurate experimental interpretation. We present a formal approach for microarray quality assessment that is based on dimension reduction of established measures of signal and noise components of expression followed by parametric multivariate outlier testing.

Results: We applied our approach to several data resources. First, as a negative control, we found that the Affymetrix and Illumina contributions to MAQC data were free from outliers at a nominal outlier flagging rate of α=0.01. Second, we created a tunable framework for artificially corrupting intensity data from the Affymetrix Latin Square spike-in experiment to allow investigation of sensitivity and specificity of quality assurance (QA) criteria. Third, we applied the procedure to 507 Affymetrix microarray GeneChips processed with RNA from human peripheral blood samples. We show that exclusion of arrays by this approach substantially increases inferential power, or the ability to detect differential expression, in large clinical studies.

Availability:  http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.html and http://bioconductor.org/packages/2.3/bioc/html/affyContam.html affyContam (credentials: readonly/readonly)

Contact:  aasare@immunetolerance.org; stvjc@channing.harvard.edu
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions
Authors: Yip Kevin Y. , Gerstein Mark
Published: November 2008

Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While there are many computational techniques proposed for this network reconstruction task, their accuracy is consistently limited by the small number of high-confidence examples, and the uneven distribution of these examples across the potential interaction space, with some objects having many known interactions and others few.

Results: To address this issue, we propose two computational methods based on the concept of training set expansion. They work particularly effectively in conjunction with kernel approaches, which are a popular class of approaches for fusing together many disparate types of features. Both our methods are based on semi-supervised learning and involve augmenting the limited number of gold-standard training instances with carefully chosen and highly confident auxiliary examples. The first method, prediction propagation, propagates highly confident predictions of one local model to another as the auxiliary examples, thus learning from information-rich regions of the training network to help predict the information-poor regions. The second method, kernel initialization, takes the most similar and most dissimilar objects of each object in a global kernel as the auxiliary examples. Using several sets of experimentally verified protein–protein interactions from yeast, we show that training set expansion gives a measurable performance gain over a number of representative, state-of-the-art network reconstruction methods, and it can correctly identify some interactions that are ranked low by other methods due to the lack of training examples of the involved proteins.

Contact:  mark.gerstein@yale.edu

Availability: The datasets and additional materials can be found at http://networks.gersteinlab.org/tse.
SIRIUS: decomposing isotope patterns for metabolite identification
Authors: Böcker Sebastian , Letzel Matthias C. , Lipták Zsuzsanna , Pervukhin Anton
Published: November 2008

Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still remain uncharacterized. Determination of the sum formula is a crucial step in the identification of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set.

Results: We present a method for determining the sum formula of a metabolite solely from its mass and the natural distribution of its isotopes. Our input is a measured isotope pattern from a high resolution mass spectrometer, and we want to find those molecules that best match this pattern. Our method is computationally efficient, and results on experimental data are very promising: for orthogonal time-of-flight mass spectrometry, we correctly identify sum formulas for >90% of the molecules, ranging in mass up to 1000 Da.

Availability: SIRIUS is available under the LGPL license at http://bio.informatik.uni-jena.de/sirius/

Contact:  anton.pervukhin@minet.uni-jena.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
YAP regulates neural progenitor cell number via the TEA domain transcription factor
Authors: Cao Xinwei , Pfaff Samuel L. , Gage Fred H.
Published: November 2008

Tight control of cell proliferation is essential for proper growth during development and for tissue homeostasis in mature animals. The evolutionarily conserved Hippo pathway restrains proliferation through a kinase cascade that culminates in the inhibition of the transcriptional coactivator YAP. Unphosphorylated YAP activates genes involved in cell proliferation and survival by interacting with a DNA-binding factor. Here we show that during vertebrate neural tube development, the TEA domain transcription factor (TEAD) is the cognate DNA-binding partner of YAP. YAP and TEAD gain of function causes marked expansion of the neural progenitor population, partly owing to their ability to promote cell cycle progression by inducing cyclin D1 and to inhibit differentiation by suppressing NeuroM. Their loss of function results in increased apoptosis, whereas repressing their target genes leads to premature neuronal differentiation. Inhibiting the upstream kinases of the Hippo pathway also causes neural progenitor overproliferation. Thus, the Hippo pathway plays critical roles in regulating neural progenitor cell number by affecting proliferation, fate choice, and cell survival.
microRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart
Authors: Liu Ning , Bezprozvannaya Svetlana , Williams Andrew H. , Qi Xiaoxia , Richardson James A. , Bassel-Duby Rhonda , Olson Eric N.
Published: November 2008

MicroRNAs (miRNAs) modulate gene expression by inhibiting mRNA translation and promoting mRNA degradation, but little is known of their potential roles in organ formation or function. miR-133a-1 and miR-133a-2 are identical, muscle-specific miRNAs that are regulated during muscle development by the SRF transcription factor. We show that mice lacking either miR-133a-1 or miR-133a-2 are normal, whereas deletion of both miRNAs causes lethal ventricular-septal defects in approximately half of double-mutant embryos or neonates; miR-133a double-mutant mice that survive to adulthood succumb to dilated cardiomyopathy and heart failure. The absence of miR-133a expression results in ectopic expression of smooth muscle genes in the heart and aberrant cardiomyocyte proliferation. These abnormalities can be attributed, at least in part, to elevated expression of SRF and cyclin D2, which are targets for repression by miR-133a. These findings reveal essential and redundant roles for miR-133a-1 and miR-133a-2 in orchestrating cardiac development, gene expression, and function and point to these miRNAs as critical components of an SRF-dependent myogenic transcriptional circuit.
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
Authors: Reinhardt Josephine A. , Baltrus David A. , Nishimura Marc T. , Jeck William R. , Jones Corbin D. , Dangl Jeffery L.
Published: November 2008

We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing) sequencing platforms, we reliably assembled genomes into large scaffolds at a fraction of the traditional cost and without use of a reference sequence. We applied this method to two isolates of the phytopathogenic bacteria Pseudomonas syringae. Sequencing and reassembly of the well-studied tomato and Arabidopsis pathogen, PtoDC3000, facilitated development and testing of our method. Sequencing of a distantly related rice pathogen, Por1_6, demonstrated our method's efficacy for de novo assembly of novel genomes. Our assembly of Por1_6 yielded an N50 scaffold size of 531,821 bp with >75% of the predicted genome covered by scaffolds over 100,000 bp. One of the critical phenotypic differences between strains of P. syringae is the range of plant hosts they infect. This is largely determined by their complement of type III effector proteins. The genome of Por1_6 is the first sequenced for a P. syringae isolate that is a pathogen of monocots, and, as might be predicted, its complement of type III effectors differs substantially from the previously sequenced isolates of this species. The genome of Por1_6 helps to define an expansion of the P. syringae pan-genome, a corresponding contraction of the core genome, and a further diversification of the type III effector complement for this important plant pathogen species.
‘I Need Help on Mondays, It’s Not My Day. The Other Days, I’m OK’.—Perspectives of Disabled Children on Inclusive Education
Authors: De Schauwer Elisabeth , Van Hove Geert , Mortier Kathleen , Loots Gerrit
Published: November 2008

This article examines the experience of inclusive education from the perspective of disabled children. We worked with the observations of, and interviews with, 15 children, aged 5–17 who go to a mainstream school. The study is set in the context of a 3‐year research project exploring the practice of inclusive education in Flanders. Here, we report on the key findings from the children’s accounts, focusing on what they had to say about themselves, what they think about school, friends, support and their future prospects.
Effects of N : P loading ratios on phytoplankton community composition, primary production and N fixation in a eutrophic lake
Authors: VREDE TOBIAS , BALLANTYNE ASHLEY , MILLE‐LINDBLOM CECILIA , ALGESTEN GRETE , GUDASZ CRISTIAN , LINDAHL SANDRA , BRUNBERG ANNA KRISTINA
Published: November 2008

1. The aim of this study was to assess the effects of different nitrogen (N) to phosphorus (P) loading ratios on phytoplankton community composition and primary production in a naturally eutrophic lake. Furthermore, the sources of N fuelling primary production were estimated using 15N stable isotope tracers.

2. A mesocosm experiment was performed with the same amount of P added to all mesocosms (similar to internal loading rates) but with a range of N additions (0–86 μm N), resulting in a gradient of N : P supply ratios.

3. Low N : P supply ratios resulted in a significant shift in the phytoplankton assemblage to a community dominated by N‐fixing cyanobacteria and a supply of atmospheric N2 estimated to be up to 60% of total supply.

4. The N : P loading ratio had no significant effect on primary production, total nitrogen (TN) concentration or particulate N concentration.

5. Our results imply that a reduced N : P ratio of the nutrient load does not necessarily result in a lower TN concentration and downstream N export due to compensation by N‐fixing cyanobacteria.
Sulphur stable isotopes can distinguish trophic dependence on sediments and plankton in boreal lakes
Authors: CROISETIÈRE LOUIS , HARE LANDIS , TESSIER ANDRÉ , CABANA GILBERT
Published: November 2008

1. Stable isotopes of carbon are useful for differentiating between freshwater food chains based on planktonic algae or benthic algae, but are reported to be of limited use for identifying food chains based on sedimentary detritus. Because data from marine systems suggest that stable isotopes of sulphur (δ34S values) have potential in this regard, we tested their utility in freshwater lakes.

2. We found that sulphate in the water column of four boreal lakes was enriched in 34S compared to the sulphur in bulk sediments from these lakes. Furthermore, within a given lake, insects known to feed on sediment (directly or via predation) had δ34S values similar to those of sediment, whereas planktonic and benthic invertebrates known to feed on suspended particles had δ34S values similar to those of sulphate in the water column.

3. Using the stable S isotope values of invertebrates that obtain their S from either the sediment or the water column as end members in a two‐source mixing model, we show that two fish species obtain their food from both planktonic and sedimentary sources. Furthermore, model results suggest that, as expected, the more benthic‐feeding fish species obtains more of its S from the sediment compartment than does the species that feeds in the water‐column.

4. Our results suggest that measurements of stable sulphur isotopes provide a means of distinguishing between members of food chains that are based in the water column from those based on sedimentary detritus. As such, they would be a useful complement to stable C isotopes that are used to distinguish between food chains based on planktonic or benthic algae.
Twentieth century increase of Scots pine radial growth in NE Spain shows strong climate interactions
Authors: MARTÍNEZ‐VILALTA J. , LÓPEZ B. C. , ADELL N. , BADIELLA L. , NINYEROLA M.
Published: November 2008

Stem radial growth responds to environmental conditions, and has been widely used as a proxy to study long‐term patterns of tree growth and to assess the impact of environmental changes on growth patterns. In this study, we use a tree ring dataset from the Catalan Ecological and Forest Inventory to study the temporal variability of Scots pine (Pinus sylvestris L.) stem growth during the 20th century across a relatively large region (Catalonia, NE Spain) close to the southern limit of the distribution of the species. Basal area increment (BAI) was modelled as a function of tree size and environmental variables by means of mixed effects models. Our results showed an overall increase of 84% in Scots pine BAI during the 20th century, consistent with most previous studies for temperate forests. This trend was associated with increased atmospheric CO2 concentrations and, possibly, with a general increase in nutrient availability, and we interpreted it as a fertilization effect. Over the same time period, there was also a marked increase in temperature across the study region (0.19 °C per decade on average). This warming had a negative impact on radial growth, particularly at the drier sites, but its magnitude was not enough to counteract the fertilization effect. In fact, the substantial warming observed during the 20th century in the study area did not result in a clear pattern of increased summer drought stress because of the large variability in precipitation, which did not show any clear time trend. But the situation may change in the future if temperatures continue to rise and/or precipitation becomes scarcer. Such a change could potentially reverse the temporal trend in growth, particularly at the driest sites, and is suggested in our data by the relative constancy of radial growth after ca. 1975, coinciding with the warmer period. If this situation is representative of other relatively dry, temperate forests, the implications for the regional carbon balance would be substantial.
The age of the grasses and clusters of origins of C4 photosynthesis
Authors: VICENTINI ALBERTO , BARBER JANET C. , ALISCIONI SANDRA S. , GIUSSANI LILIANA M. , KELLOGG ELIZABETH A.
Published: November 2008

At high temperatures and relatively low CO2 concentrations, plants can most efficiently fix carbon to form carbohydrates through C4 photosynthesis rather than through the ancestral and more widespread C3 pathway. Because most C4 plants are grasses, studies of the origin of C4 are intimately tied to studies of the origin of the grasses. We present here a phylogeny of the grass family, based on nuclear and chloroplast genes, and calibrated with six fossils. We find that the earliest origins of C4 likely occurred about 32 million years ago (Ma) in the Oligocene, coinciding with a reduction in global CO2 levels. After the initial appearance of C4 species, photosynthetic pathway changed at least 15 more times; we estimate nine total origins of C4 from C3 ancestors, at least two changes of C4 subtype, and five reversals to C3. We find a cluster of C4 to C3 reversals in the Early Miocene correlating with a drop in global temperatures, and a subsequent cluster of C4 origins in the Mid‐Miocene, correlating with the rise in temperature at the Mid‐Miocene climatic optimum. In the process of dating the origins of C4, we were also able to provide estimated times for other major events in grass evolution. We find that the common ancestor of the grasses (the crown node) originated in the upper Cretaceous. The common ancestor of maize and rice lived at 52 ± 8 Ma.
Nutrient constraints to tropical agroecosystem productivity in long‐term degrading soils
Authors: NGOZE SOLOMON , RIHA SUSAN , LEHMANN JOHANNES , VERCHOT LOUIS , KINYANGI JAMES , MBUGUA DAVID , PELL ALICE
Published: November 2008

Soil degradation is one of the most serious threats to sustainable crop production in many tropical agroecosystems where extensification rather than intensification of agriculture has occurred. In the highlands of western Kenya, we investigated soil nitrogen (N) and phosphorus (P) constraints to maize productivity across a cultivation chronosequence in which land‐use history ranged from recent conversion from primary forest to 100 years in continuous cropping. Nutrient treatments included a range of N and P fertilizer rates applied separately and in combination. Maize productivity without fertilizer was used as a proxy measure for indigenous soil fertility (ISF). Soil pools of mineral nitrogen, strongly bound P and plant‐available P decreased by 82%, 31% and 36%, and P adsorption capacity increased by 51% after 100 years of continuous cultivation. For the long rainy season (LR), grain yield without fertilizer declined rapidly as cultivation age increased from 0 to 25 years and then gradually declined to a yield of 1.6 Mg ha−1, which was maintained as time under cultivation increased from 60 to 100 years. LR grain yield in the old conversions was only 24% of the average young conversion grain yield (6.4 Mg ha−1). Application of either N or P alone significantly increased grain yield in both the LR and short rainy (SR) seasons, but only application of 120 kg N ha−1 on the old conversion increased yield by >1 Mg ha−1. In both SR and LR, there was a greater average yield increment response to N and P when applied together (ranging from 1 to 3.8 Mg ha−1 for the LR), with the greatest responses on the old conversions. The benefit–cost ratio (BCR) for applying 120 kg N ha−1 alone was <1 except on the old conversions, while BCRs were>1 for applying 25 kg P ha−1 alone at all levels of conversion for both seasons. Application of both N (120 kg N ha−1) and P (25 kg P ha−1) on the old conversions resulted in the greatest BCRs. This study clearly indicates that maize productivity responses to N and P fertilizer are significantly affected by the age of cultivation and its influence on ISF, but that loss of productivity can be restored rapidly when these limiting nutrients are applied. Management strategies should consider ISF and economic factors to determine optimal N and P input requirements for achieving and sustaining profitable crop production on degraded soils.
Immediate and long‐term nitrogen oxide emissions from tropical forest soils exposed to elevated nitrogen input
Authors: KOEHLER BIRGIT , CORRE MARIFE D. , VELDKAMP EDZO , WULLAERT HANS , WRIGHT S. JOSEPH
Published: November 2008

Tropical nitrogen (N) deposition is projected to increase substantially within the coming decades. Increases in soil emissions of the climate‐relevant trace gases NO and N2O are expected, but few studies address this possibility. We used N addition experiments to achieve N‐enriched conditions in contrasting montane and lowland forests and assessed changes in the timing and magnitude of soil N‐oxide emissions. We evaluated transitory effects, which occurred immediately after N addition, and long‐term effects measured at least 6 weeks after N addition. In the montane forest where stem growth was N limited, the first‐time N additions caused rapid increases in soil N‐oxide emissions. During the first 2 years of N addition, annual N‐oxide emissions were five times (transitory effect) and two times (long‐term effect) larger than controls. This contradicts the current assumption that N‐limited tropical montane forests will respond to N additions with only small and delayed increases in soil N‐oxide emissions. We attribute this fast and large response of soil N‐oxide emissions to the presence of an organic layer (a characteristic feature of this forest type) in which nitrification increased substantially following N addition. In the lowland forest where stem growth was neither N nor phosphorus (P) limited, the first‐time N additions caused only gradual and minimal increases in soil N‐oxide emissions. These first N additions were completed at the beginning of the wet season, and low soil water content may have limited nitrification. In contrast, the 9‐ and 10‐year N‐addition plots displayed instantaneous and large soil N‐oxide emissions. Annual N‐oxide emissions under chronic N addition were seven times (transitory effect) and four times (long‐term effect) larger than controls. Seasonal changes in soil water content also caused seasonal changes in soil N‐oxide emissions from the 9‐ and 10‐year N‐addition plots. This suggests that climate change scenarios, where rainfall quantity and seasonality change, will alter the relative importance of soil NO and N2O emissions from tropical forests exposed to elevated N deposition.
Wine cluster formation in New Zealand: operation, evolution and impact
Authors: Dana Leo P. , Winstone Kate E.
Published: November 2008

This paper analyses the Waipara wine cluster, located in the South Island of New Zealand, in relation to formation, operation, evolution and impact. The unique methodological approach of this research is that it analyses the current and desired future state of the cluster and secondly examines the cluster in relation to both the domestic and international markets. Key findings from the research include a greater understanding of the relationships between cluster members, the operation of cluster, problems within the cluster and how the cluster operates for both domestic and international markets. The research lends itself to a new definition of internationalisation –‘direct and indirect methods of increasing the likelihood of international sales’– and also provides new insights for cluster theory, wine clusters and the wine industry in general. Some of the practices detailed have use in the wider wine community of the world, making the paper of interest to a wide audience.
Cross‐cultural factors in disclosure of intimate partner violence: an integrated review
Authors: Montalvo‐Liendo Nora
Published: November 2008

Title. Cross‐cultural factors in disclosure of intimate partner violence: an integrated review.

Aim. This paper is a report of an integrated review to identify cross‐cultural factors that have an impact on women’s disclosure of intimate partner violence, specifically related to Mexican‐American women.

Background. Intimate partner violence was once recognized as a private matter. Disclosure is a complex concept; furthermore in our multi‐cultural society, a woman’s decision whether or not to disclose abuse can be attributed to several factors influenced by her culture.

Data sources. The World Wide Web and multiple databases including Academic Premier, Cumulative Index of Nursing and Allied Health Literature (CINAHL), PsychArticles, PsychInfo, Medline, Eric, MedicLatina, and Psychology and Behavioral Science Collection were searched for studies published between 1996 and 2007.

Methods. A search was conducted using databases including the CINAHL, PsychINFO, MEDLINE, ERIC and MedicLatina. Both qualitative and quantitative studies published between May 1996 and July 2007 were included. Forty‐two studies were included in the review. Appraisal of study quality was not undertaken.

Results. Fear was the most common cross‐cultural factor interfering with disclosure. Most of the literature examines factors influencing and interfering with disclosure of abuse among white and African‐American women. Only one study was found to include a sample of Mexican‐American women.

Conclusion. Increased efforts are needed to understand disclosure of intimate partner violence in minority women so that service providers can tailor services and ways to encourage disclosure with appropriate strategies based on women’s culture. Further research is needed to understand the lived experiences of minority women, including Mexican‐American women living in intimate partner violence.
Being a personal preceptor for nursing students: Registered Nurses’ experiences before and after introduction of a preceptor model
Authors: Hallin Karin , Danielson Ella
Published: November 2008

Title.  Being a personal preceptor for nursing students: Registered Nurses’ experiences before and after introduction of a preceptor model.

Aim.  This paper is a report of a study to compare Registered Nurses’ experiences of acting as personal preceptors for nursing students in the year 2000 with the year 2006 and explores relationships between preceptors’ experiences and personal/clinical characteristics.

Background.  Preceptoring is experienced as stressful and challenging. How successful preceptors are in this role depends largely on the support they receive. Knowledge about preceptors’ experiences over time and in relation to a preceptor model is limited.

Method.  Data were collected by questionnaire in 2000 (n = 113) and 2006 (n = 109) with preceptor groups in a hospital in Sweden before and after introduction of a preceptor model. Data were analysed with descriptive and correlational statistics using parametric and non‐parametric methods.

Findings.  Statistically significant improvements were noted in preceptors’ experiences between 2000 and 2006. Statistically significantly more preceptors in 2006 reported that they felt prepared for their role and felt support from teachers, colleagues, chief nurses and enrolled nurses. Least improvement was seen in relation to the questionnaire items workload, constructive feedback and support in linking research results to practice. A strong positive relationship existed between preceptors’ experiences of the preceptor role and the level of interest in preceptoring.

Conclusion.  The preceptor model offers a way to support and facilitate preceptors and to develop co‐operation between university and hospital. Future research should focus on students’ experiences, experiences of first‐time preceptors, head preceptors and teachers from a longitudinal perspective.
The gaseous mediator, hydrogen sulphide, inhibits in vitro motor patterns in the human, rat and mouse colon and jejunum
Authors: Gallego D. , Clavé P. , Donovan J. , Rahmati R. , Grundy D. , Jiménez M. , Beyak M. J.
Published: November 2008

Abstract  Hydrogen sulphide (H2S) has been recently proposed as a transmitter in the brain and peripheral tissues. Its role in the gastrointestinal tract is still unknown despite some data which suggest an involvement mediating smooth muscle relaxation. The aim of this study was to investigate the effect of this gas on intestinal segments from mouse jejunum and colon, and muscular strips from the human and rat colon. In isolated segments of mouse colon and jejunum, bath applied sodium hydrogen sulphide (NaHS) (a H2S donor) caused a concentration‐dependent inhibition of spontaneous motor complexes (MCs) (IC50 121 μmol L−1 in the colon and 150 μmol L−1 in the jejunum). This inhibitory effect of NaHS on MCs was (i) unaffected by tetrodotoxin (TTX), capsaicin, pyridoxal‐phosphate‐6‐azophenyl‐2′,4′‐disulfonate and N‐nitro‐l‐arginine suggesting a non‐neural effect and (ii) significantly reduced by apamin 3 μmol L−1. NaHS concentration‐dependently inhibited the spontaneous motility in strips from human colon (IC50 261 μmol L−1) and rat colon (IC50 31 μmol L−1). The inhibitory effect of NaHS on colonic strips was (i) unaffected by the neural blocker TTX (1 μmol L−1) with IC50 183 μmol L−1 for the human colon and of 26 μmol L−1 for the rat colon and (ii) significantly reduced by glybenclamide (10 μmol L−1), apamin (3 μmol L−1) and TEA (10 mmol L−1) with IC50 values of 2464, 1307 and 2421 μmol L−1 for human strips, and 80, 167 and 674 μmol L−1 for rat strips respectively. We conclude that H2S strongly inhibits in vitro intestinal and colonic motor patterns. This effect appears to be critically dependent on K channels particularly apamin‐sensitive SK channels and glybenclamide‐sensitive K (ATP) channels.
An fMRI investigation of working memory and sadness in females with bipolar disorder: a brief report
Authors: Deckersbach Thilo , Rauch Scott L , Buhlmann Ulrike , Ostacher Michael J , Beucke Jan‐Carl , Nierenberg Andrew A , Sachs Gary , Dougherty Darin D
Published: November 2008

Objective: Functional magnetic resonance imaging (fMRI) studies have documented abnormalities in the dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex in bipolar disorder in the context of working memory tasks. It is increasingly recognized that DLPFC regions play a role in mood regulation and the integration of emotion and cognition. The purpose of the present study was to investigate with fMRI the interaction between acute sadness and working memory functioning in individuals with bipolar disorder.

Methods: Nine depressed individuals with DSM‐IV bipolar I disorder (BP‐I) and 17 healthy control participants matched for age, gender, education, and IQ completed a 2‐back working memory paradigm under no mood induction, neutral state, or acute sadness conditions while undergoing fMRI scanning. Functional MRI data were analyzed with SPM2 using a random‐effects model.

Results: Behaviorally, BP‐I subjects performed equally well as control participants on the 2‐back working memory paradigm. Compared to control participants, individuals with BP‐I were characterized by more sadness‐specific activation increases in the left DLPFC (BA 9/46) and left dorsal anterior cingulate (dACC).

Conclusions: Our study documents sadness‐specific abnormalities in the left DLPFC and dACC in bipolar disorder that suggest difficulties in the integration of emotion (sadness) and cognition. These preliminary findings require further corroboration with larger sample sizes of medication‐free subjects.
Neuropsychological and electrophysiological indices of neurocognitive dysfunction in bipolar II disorder
Authors: Andersson Stein , Barder Helene E , Hellvin Tone , Løvdahl Hans , Malt Ulrik F
Published: November 2008

Objectives:  There are conflicting findings regarding the nature and degree of neurocognitive dysfunction in bipolar II disorder (BD II). The aim of this study was to describe different levels of neurocognitive functioning in BD II by combining behavior‐based methods (neuropsychological testing) and event‐related potentials (ERP).

Methods:  Twenty‐five consecutively referred outpatients fulfilling DSM‐IV criteria for BD II and 28 matched controls performed a neuropsychological test battery targeting working memory/attention, executive functions, verbal and visual memory, and psychomotor speed. In addition, ERPs for measuring early and controlled stages of information processing were recorded using a duration mismatch negativity (MMN) paradigm and a three‐tone auditory oddball paradigm.

Results:  Compared to controls, BD II patients’ performance was significantly impaired on all neuropsychological measures, except for phonemic verbal fluency, with moderate to strong effect sizes ranging from 0.62 to 1.34. The ERP results indicate dysfunctions in early stages of information processing, showing a significant MMN latency increase and attenuated frontal amplitudes in BD II patients. Female patients showed increased P3a latency compared to female controls, but no group differences were found for P3b latency or amplitude, the ERP component expressing controlled information processing.

Conclusions:  The functional significance of neuropsychological impairment is discussed. Differences regarding some aspects of executive function may be related to psychomotor speed, and not primarily to dysexecutive functioning. ERP results must be interpreted with caution, but the differences found in MMN latency and amplitudes may be related to fronto‐temporal circuitry underlying pre‐attentive stimulus change detection as measured by MMN, and are discussed in relation to previous research on MMN in other neuropsychiatric conditions.
Cognitive functioning in euthymic bipolar I and bipolar II patients
Authors: Dittmann Sandra , Hennig‐Fast Kristina , Gerber Sonja , Seemüller Florian , Riedel Michael , Emanuel Severus W , Langosch Jens , Engel Rolf R , Möller Hans‐Jürgen , Grunze Heinz C
Published: November 2008

Objective:  There is growing evidence of cognitive impairment as a trait factor in bipolar disorder. The generalizability of this finding is limited because previous studies have either focussed exclusively on bipolar I disorder or have analysed mixed patient groups. Thus, it is still largely unknown whether bipolar II patients perform differently from bipolar I patients on measures of cognitive functioning.

Methodology:  A total of 65 patients with bipolar I disorder, 38 with bipolar II disorder, and 62 healthy controls participated in the study. Patients had to be euthymic for at least one month. Clinical and demographic variables were collected in a clinical interview and with the Structured Clinical Interview for DSM‐IV. Cognitive functioning was assessed using a neuropsychological battery. Univariate and multivariate analyses of variance were conducted for analyzing possible differences between the groups.

Results:  The multivariate analysis of covariance (MANCOVA) indicated overall differences in neuropsychological performance between the three groups (Pillai Spur: F 1.96, p = 0.003). Post hoc comparisons revealed that patients with bipolar I disorder showed significantly lower scores in psychomotor speed, working memory, verbal learning, delayed memory, and executive functions than healthy controls. Patients with bipolar II disorder showed significant deficits in psychomotor speed, working memory, visual/constructional abilities, and executive functions compared to controls, but not on verbal learning and delayed memory. The two patient groups did not differ significantly from each other on any domain tested.

Conclusion:  These results support a similar pattern of cognitive deficits in both subtypes of bipolar disorder.
Codeposition of dNTPs Detection for Rapid LAMP‐based Sexing of Bovine Embryos
Authors: Zhang Z‐P , Zhang Y , Liu J‐P , Zhang J‐T , An Z‐X , Quan F‐S , Zhang L , Cai X , Pu SWJ
Published: November 2008

Contents

Loop‐mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method with high specificity and rapidity under isothermal conditions. According to the LAMP method, a rapid and simple detection system was established for bovine embryo sexing. Two sets of primers were designed by targeting the bovine male‐specific sequence and bovine common sequence respectively. The reaction condition of the detection system was optimized within 60 min under isothermal conditions of 65°C by detection of the reaction mixture on agarose gel. Especially, the primers F2 and B2 could replace the F3 and B3 as outer primers, making the primer design simpler and the amplification efficiency higher. Additionally, codeposition of dNTPs was firstly performed to detect the reaction products by addition of 1 μl 0.1 mm CuSO4, the visible ring‐shaped deposit was found in the middle of the reaction tube with negative mixture. It could be employed as an alternative method in the detection of the reaction products in place of the time‐consuming electrophoresis or the turbidity meter. Furthermore, the embryo sexing system was carried out in the embryo transfer and achieved 98% of efficiency and 99.5% of accuracy.
Expression of Interferon‐tau mRNA in Bovine Embryos Derived from Different Procedures
Authors: Yao N , Wan P‐C , Hao Z‐D , Gao F‐F , Yang L , Cui M‐S , Wu Y , Liu J‐H , Liu S , Chen H , Zeng S‐M
Published: November 2008

Contents

Interferon‐tau (IFN‐τ) is a secreted conceptus protein which plays a critical role in the establishment of ruminant pregnancy by its antiluteolytic and antiviral effects. In the present study, we hypothesized that IFN‐τ expression was temporally and spatially regulated in different pre‐implantation embryos and the levels of IFN‐τ expression were different among bovine embryos derived from parthenogenetic activation (PA), in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT). By using in situ hybridization with Digoxingenin (DIG)‐labelled IFN‐τ cDNA as a probe, we detected IFN‐τ mRNA in bovine embryos from days 3 to 9 in culture. However, the timing of the initiation of IFN‐τ mRNA expression was different among PA, IVF and SCNT embryos. Interferon‐τ mRNA was first expressed in 16‐cell stage IVF embryos on day 4, in SCNT morula on day 5 and early PA blastocyst on day 6. Semi‐quantitative RT‐PCR analysis showed that the expression levels of IFN‐τ mRNA did not differ significantly among IVF, SCNT and PA embryos on day 7. In addition, freezing and thawing did not have a major impact either on IFN‐τ mRNA expression in IVF or in vivo‐produced bovine blastocysts.
Formation of Corpora Lutea and Central Luteal Cavities and Their Relationship with Plasma Progesterone Levels and Other Metabolic Parameters in Dairy Cattle
Authors: Perez‐Marin C
Published: November 2008

Contents

The corpus luteum (CL) may be looked upon as a compact or cavitary structure. A number of papers have addressed the relationship between CL type and parameters such as fertility or progesterone levels. The present study assessed the morphological and functional sequence observed in cows with different CL types, comparing pre‐ovulatory follicle size, progesterone levels, luteal tissue formation and some blood biochemical parameters (calcium, albumin, inorganic phosphorus, glucose, magnesium, copper and zinc), oestrus cycle length and oestrus expression, as a function of CL type. Twenty‐eight lactating dairy cows from two commercial dairy farms in southern Spain were studied. Oestrus detection was performed by monitoring daily oestrus behaviour, and artificial insemination (AI) was perfomed using the AM/PM rule. Ovaries and uterus were sonographically examined and blood samples were collected to measure progesterone and various biochemical parameters. There was a slight tendency towards the appearance of luteal cavities when pre‐ovulatory follicles were larger (1.9 ± 0.2 vs 1.7 ± 03; p = 0.074). Fertility was not affected by cavity presence (cavity = 42.9% and compact = 57.1%; n.s.). Luteal tissue and function were not modified as a function of CL type. Cows with luteal cavities displayed significantly higher levels of albumin, suggesting a possible metabolic influence on the formation of these structures, although specific research is required to confirm this observation.
Transcriptional regulatory defects in the first intron of Bruton’s tyrosine kinase
Authors: Shin Dong‐Min , Jo Eun‐Kyeong , Kanegane Hirokazu , Futatani Takeshi , Zhao Meina , Song Chang‐Hwa , Yamagishi Atsushi , Miyawaki Toshio
Published: November 2008

Background: X‐linked agammaglobulinemia (XLA), characterized by the early onset of recurrent bacterial infections, profound hypogammaglobulinemia, and a markedly diminished number of peripheral B lymphocytes, is caused by mutations in the Bruton’s tyrosine kinase (BTK) gene. The >600 unique mutations identified to date include single base pair substitutions, small insertions or deletions, and gross deletions. A few cases, however, have been found to have no mutations in the coding region even with reduced BTK mRNA or protein expression. Mutations in intron 1 positions +5 (G→A) and +6 (T→G) of the BTK gene have been identified, and these changes were associated with reduced transcriptional activity.

Methods: In the present study a novel mutation in intron 1 position +5 (G→T) was identified in a Japanese patient with XLA. The reporter constructs containing these mutations were made, and the reporter activities were measured using a luciferase assay.

Results: All the mutant constructs were demonstrated to have reduced transcriptional activity.

Conclusions: Positions +5 and +6 in intron 1 of the BTK gene are critical for transcriptional activity, and defects in these regions cause XLA.