bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of methanogens in ruminants in Queensland
Authors: Ouwerkerk D. , Turner A. F. , Klieve A. V.
Published: June 2008

Methane emissions from ruminant livestock represent a loss of carbon during feed conversion, which has implications for both animal productivity and the environment because this gas is considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in different breeds of cattle and sheep, as well as in response to different diets, is required. A study was undertaken using the molecular techniques denaturing gradient gel electrophoresis, DNA cloning and DNA sequence analysis to define the extent of diversity among methanogens in ruminants, particularly Bos indicus cross cattle, on differing forages in Queensland. It was found that the diversity of methanogens in forage-fed cattle in Queensland was greater than in grain-fed cattle but there was little variability in methanogen community composition between cattle fed different forages. The species that dominate the rumen microbial communities of B. indicus cross cattle are from the genus Methanobrevibacter, although rumen-fluid inoculated digestors fed Leucaena leucocephala leaf were populated with Methanosphaera-like strains, with the Methanobrevibacter-like strains displaced. If ruminant methane emissions are to be reduced, then antimethanogen bioactives that target both broad groups of ruminant methanogens are most likely to be needed, and as a part of an integrated suite of approaches that redirect rumen fermentation towards other more useful end products.
Water and feed intake responses of sheep to drinking water temperature in hot conditions
Authors: Savage D. B. , Nolan J. V. , Godwin I. R. , Mayer D. G. , Aoetpah A. , Nguyen T. , Baillie N. D. , Rheinberger T. E. , Lawlor C.
Published: June 2008

When live-export sheep from Australia arrive in the Middle East during the northern summer months, they may be offered drinking water at temperatures exceeding 40°C. There is little published research to indicate whether drinking water temperature is important in managing heat stress in sheep or its effect on their health and welfare. Three studies were conducted with Merino wethers in climate-controlled rooms to investigate: (i) responses to drinking water temperatures of 20°C, 30°C and 40°C in a cool (20°C) and hot (40°C) environment, (ii) preferences for drinking water temperature at 20°C or 30°C when in a hot or cool environment and (iii) effects of water restriction when offered hot water (40°C) in a hot environment. Sheep assigned to the hot room had significantly higher respiration rates than those assigned to the cool room. In the cool environment, water intakes were the same when water temperatures were 20°C, 30°C or 40°C; however, when the sheep were given a choice between drinking water at 20°C and 30°C, they preferred (P < 0.05) to drink water at 20°C. In the hot environment, water intake increased as drinking water temperature increased, and sheep preferred to drink water at 30°C rather than 20°C. When the availability of 40°C drinking water was restricted (to ~10% of liveweight) in the hot environment, sheep had higher respiration rates than those offered unlimited water.
Usefulness of extraperitoneal laparoscopic paraaortic lymphadenectomy for lymph node recurrence in gynecologic malignancy
Authors: GIL‐MORENO ANTONIO , FRANCO‐CAMPS SILVIA , DÍAZ‐FEIJOO BERTA , PÉREZ‐BENAVENTE ASUMPCIÓ , MARTÍNEZ‐PALONES JOSÉ M. , DEL CAMPO JOSÉ M. , PARERA MARTA , VERGÉS RAMONA , CASTELLVÍ JOSEP , XERCAVINS JORDI
Published: June 2008

Objective. The aim of this study was to evaluate the safety and feasibility of extraperitoneal laparoscopic paraaortic lymphadenectomy for suspected lymph node recurrence of gynecological cancers. Design. Descriptive study. Setting. Unit of Gynecologic Oncology of an acute‐care teaching hospital in Barcelona, Spain. Population. Between December 2002 and October 2007, eight women underwent extraperitoneal laparoscopic paraaortic lymphadenectomy for suspected lymph node recurrence, detected by magnetic resonance image (MRI), computed tomography (CT) scan or 18F‐fluorodeoxyglucose positron emission tomography (PET) scanning. The suspicious nodes were removed through an extraperitoneal laparoscopic approach. Resuts. The median age of patients was 66.5 years (range: 54–74). The median operating time was 157.5 minutes (range: 120–240). The median blood loss was 112.5 mL (range: 50–150). The mean nodal yield was 9.4±4.72 (range: 1–16). There were no intraoperative or postoperative complications. The median hospital stay was two days. Histological examination revealed metastasis in seven of eight patients. Conclusions. The extraperitoneal laparoscopic paraaortic lymphadenectomy for lymph node recurrence of gynecological cancers is a safe and feasible procedure which should be considered where there is isolated involvement of retroperitoneal lymph nodes. This procedure is a minimally invasive technique that allows an excellent approach to the paraaortic lymph nodes.
Female genital mutilation among antenatal care and contraceptive advice attendees in Sweden
Authors: LITORP HELENA , FRANCK MARTINA , ALMROTH LARS
Published: June 2008

Objective. To explore knowledge of, attitudes toward and practice of female genital mutilation (FGM) among women originally from countries where FGM is customary attending antenatal care and contraceptive advice in Sweden. Methods. Women in reproductive age living in Sweden who originate from countries where FGM is practiced coming for antenatal care or contraceptive advice at two maternity welfare centers in Stockholm were asked to participate. Interview administered questionnaires and gynecological examination were used for data collection. The data were analyzed by descriptive statistics. Results. Out of 49 women asked, 40 women agreed to participate, of whom 37 had undergone FGM. Most FGM operations had been performed by doctors or midwives. Half of the Muslim women said FGM was allowed by their religion. All women reporting to have undergone ‘sunna’, an allegedly mild form, had extensive damage to their genitals. At gynecological examination three cases of reinfibulation were detected, of which two had been performed after delivery in Sweden. Twenty‐nine women had daughters and three had let their daughters undergo FGM, all of them before settling in Sweden. Problems related to delivery and sexual intercourse were the most commonly mentioned complications of FGM. Conclusions. The reliability of the self‐reported form of FGM is low, which may have implications for research, interventions and health care. Although many women express negative attitudes toward FGM and know about serious complications, the religious justifications, the practice of FGM on daughters, reinfibulation on adults and medicalization of the practice indicate attitudes that favor of the continued practice of FGM.
Outcome of planned home births compared to hospital births in Sweden between 1992 and 2004. A population‐based register study
Authors: LINDGREN HELENA E. , RÅDESTAD INGELA J. , CHRISTENSSON KYLLIKE , HILDINGSSON INGEGERD M.
Published: June 2008

Objective. The aim of this population‐based study was to measure the risk of adverse outcome for mother and child in planned home births in a Swedish population irrespective of where the birth actually occurred, at home or in hospital after transfer. Design. A population‐based study using data from the Swedish Medical Birth Register. Setting. Sweden 1992–2004. Participants. A total of 897 planned home births were compared with a randomly selected group of 11,341 planned hospital births. Main outcome measures. Prevalence of mortality and morbidity among mothers and children, emergency conditions, instrumental and operative delivery and perineal lacerations were compared. Results. During this period in Sweden the neonatal mortality rate was 2.2 per thousand in the home birth group and 0.7 in the hospital group (RR 3.6, 95% CI 0.2–14.7). No cases of emergency complications were found in the home birth group. The risk of having a sphincter rupture was lower in the planned home birth group (RR 0.2, 95% CI 0.0–0.7). The risk of having a cesarean section (RR 0.4, 95% CI 0.2–0.7) or instrumental delivery (RR 0.3, 95% CI 0.2–0.5) was significantly lower in the planned home birth group. Conclusion. In Sweden, between 1992 and 2004, the intrapartum and neonatal mortality in planned home births was 2.2 per thousand. The proportion is higher compared to hospital births but no statistically significant difference was found. Women in the home birth group more often experienced a spontaneous birth without medical intervention and were less likely to sustain pelvic floor injuries.
Education for sustainability in university studies: A model for reorienting the curriculum
Authors: Junyent Mercè , de Ciurana Anna M. Geli
Published: June 2008

A decisive factor for achieving a culture of sustainability is university training for future professionals. The aim of this article is to bring new elements to the process of reorienting university studies towards sustainability. Presented here is the ACES model (Curriculum Greening of Higher Education, acronym in Spanish), which is the result of a project involving a network of 11 European and Latin American universities. The methodology of the project is based on participatory action research. The ACES model is defined by 10 characteristics, detailed in this article, which can orientate a diagnosis of the level of curriculum greening and the design and application of the strategies and actions in order to facilitate incorporating the sustainability dimension in higher education. The potentialities and limitations found are also discussed. The ACES model has started a process for reorienting higher education studies towards sustainability.
Do new information and communications technologies have a role to play in the achievement of education for all?
Authors: Leach Jenny
Published: June 2008

Many commentators have suggested that the use of new information and communications technologies (ICTs) has significant potential in providing access to, and improving the quality of, teacher education. Such an idea is particularly relevant for the Global South, it is argued, where tens of thousands more qualified teachers are required if universal primary education (UPE) is to be achieved. This article explores six arguments commonly used to critique the relevance of ICT for development, encompassing technical, cost, philosophical, cultural and pedagogic issues. The arguments are categorised as the ‘technological’ view; the ‘donor’ view; the ‘anthropological’ view; the ‘standard’ view; the ‘individual’ view; and the ‘transmissional’ view. Drawing on empirical research into ICT and teacher education in sub‐Saharan Africa, including the work of the Digital Education Enhancement Project, six responses are used to review these arguments (‘developmental’, ‘democratic’, ‘cultural’, ‘deep’, ‘community’ and ‘pedagogic’). The author concludes that these contemporary data offer new ways of thinking about such debates and concludes with recommendations for policy makers, educators and the donor community.
Mathematics and science choice following introduction of compulsory study profiles into Dutch secondary education
Authors: van Langen Annemarie , Rekers‐Mombarg Lyset , Dekkers Hetty
Published: June 2008

Since 1998, upper level secondary education pupils in the Netherlands are required to choose one of four study profiles with their own specific and fixed combinations of final examination subjects. With the aid of multilevel analyses, the extent to which this situation has led to changes in the determinants of mathematics and science choice (i.e. selection of a science profile) is examined for more than 3500 pupils. From a meritocratic perspective, the relative contributions of background characteristics versus personal aptitude are examined. The introduction of the study profiles appears to have produced sharper lines with respect to sex and socio‐economic status. Optimal use is thus not made of existing science talent.
Chronic hydrocephalus after neurosurgical and endovascular treatment of ruptured intracranial aneurysms
Authors: Jartti P. , Karttunen A. , Isokangas J.-M. , Jartti A. , Koskelainen T. , Tervonen O.
Published: June 2008

Background: Chronic hydrocephalus is a common sequela of subarachnoid hemorrhage (SAH). The technical procedure used to treat intracranial aneurysms, whether neurosurgical clipping or endovascular coiling, may lead to differences in the incidence of chronic posthemorrhagic hydrocephalus.

Purpose: To compare the effects of early neurosurgical and early endovascular treatment on the development of chronic hydrocephalus in patients with SAH.

Material and Methods: A retrospective study included 102 clipped and 107 coiled patients with aneurysmal SAH. Clinical condition at admission and shunt dependence were verified from patient data records. The initial and follow-up computed tomography (CT) images were reviewed, and the amount and distribution of blood and the occurrence of hydrocephalus were registered. The values of the cella media index and the width of the third ventricle were calculated. Statistical analysis of the data was performed.

Results: No statistically significant differences in the incidence of chronic hydrocephalus or the need for shunting emerged between the treatment groups. After clipping 35% and after coiling 39% of the patients developed chronic hydrocephalus. Twenty-nine percent of the clipped and 31% of the coiled patients underwent a shunt operation.

Conclusion: The treatment method used for acutely ruptured intracranial aneurysms, i.e., neurosurgical clipping or endovascular coiling, has no statistically significant effect on the development of chronic hydrocephalus.
Fat-suppressed t2* sequences for routine 3.0-tesla lumbar spine magnetic resonance imaging: a preliminary report
Authors: McKinney A. M. , Gadani S. , Palmer C. S. , Vidarsson L.
Published: June 2008

Background: Clear depiction of the ligamentum flavum on routine lumbar magnetic resonance imaging (MRI) is essential in accurately describing the extent of degenerative disease. In routine, noncontrast evaluations, focal fatty deposition or hemangiomas can be difficult to distinguish from malignant foci on fast spin-echo (FSE) T2-weighted images.

Purpose: To describe the use of T2* fast field echo (T2FFE) in combination with spectral presaturation inversion recovery (SPIR) fat suppression for noncontrast, routine lumbar spine outpatient MR imaging at 3.0 Tesla (3T).

Material and Methods: An axial gradient echo (GE) T2FFE sequence was combined with SPIR fat suppression (T2FFE-SPIR), via a 3T Philips Intera (Philips Medical Systems, Best, The Netherlands) scanner, and added to the routine, noncontrast lumbar MRI examinations, which included sagittal FSE T1-weighted (T1WI), T2-weighted (T2WI), short-tau inversion recovery (STIR), and axial FSE T2WI. The sequence was performed in over 500 patients over a 1-year period, without intravenous contrast, and with slice thickness and planes of section identical to the axial FSE T1WI and T2WI images. The sequence typically lasted about 4.5–6 min.

Results: The use of T2FFE-SPIR enabled visualization of the ligamentum flavum in degenerative disease, and the exclusion of focal fatty lesions on FSE T2WI. Other benefits included: the identification of malignant foci, the uncommon detection of hemorrhage, and the elimination of spurious flow voids. Several brief examples are provided to demonstrate the utility of this technique.

Conclusion: The addition of T2FFE-SPIR to routine, noncontrast protocols in outpatients could provide further confidence in the visualization of the ligamentum flavum in degenerative disease, and can exclude malignancy in T2-bright areas of focal fatty marrow. Larger studies would be helpful to evaluate the accuracy of this technique versus FSE techniques in depicting degenerative, malignant, or inflammatory disorders.
The prognostic role of magnetic resonance imaging and single-photon emission computed tomography in viral encephalitis
Authors: Misra U. K. , Kalita J. , Srivastav A. , Pradhan P. K.
Published: June 2008

Background: There is a paucity of studies evaluating the prognostic role of magnetic resonance imaging (MRI) and single-photon emission computed tomography (SPECT) changes in viral encephalitis.

Purpose: To study MRI and SPECT changes in patients with viral encephalitis, and to correlate these changes with clinical findings and outcome.

Material and Methods: During 1997–2006, 31 encephalitis patients (aged 2–60 years; nine females, 22 males) underwent both MRI and SPECT studies. Their demographic and clinical data and 6-month outcome were recorded. For the diagnosis of encephalitis, polymerase chain reaction (PCR) and IgM enzyme-linked immunosorbent assay (ELISA) were carried out. Cranial MRI was done on a 1.5T scanner, and 99mTc ethylene cysteine dimer (ECD) SPECT using a gamma camera. Outcome was defined at 6 months as complete, partial, or poor recovery.

Results: 19 patients had Japanese encephalitis (JE), one had herpes simplex encephalitis (HSE), and 11 had nonspecific encephalitis. Movement disorders were present in 21, parkinsonian features in 19, and dystonia in 16 patients. MRI was abnormal in 20 patients, and revealed thalamic involvement in 17, basal ganglia in eight, brainstem in 11, and cortical in two. SPECT revealed hypoperfusion in 22 patients, which was cortical in 11, thalamic in 10, basal ganglia in six, and midbrain in one. Cortical involvement was more frequently found by SPECT and brainstem involvement by MRI. Outcome of encephalitis did not differ in the different groups of encephalitis and MRI changes.

Conclusion: MRI and SPECT show a spectrum of findings in encephalitis, but these do not correlate with 6-month outcome.
Evolution of lakes in the Huron basin: Deglaciation to present
Authors: Michael Lewis C. F. , Karrow Paul F. , Blasco Stefan M. , McCarthy Francine M. G. , King John W. , Moore Theodore C. , Rea David K.
Published: June 2008

Water bodies, ancestral to the present lakes including Lake Huron, first appeared in the southern Great Lakes basin about 15,500 14C years (18,800 cal years) BP during the oscillatory northward retreat of the last (Laurentide) ice sheet from its maximum position south of the Great Lakes watershed. Glacial lakes, impounded by a retreating ice margin on their northern shores, were continuously present after 13,000 14C (15,340 cal) BP for 3000 14C (3900 cal) years. Drainage routings varied in time through the Erie and Michigan basins to the Mississippi River system, a probable source for colonizing aquatic organisms, then to the Ontario basin, and finally northeastward to the Ottawa River valley via the isostatically-depressed North Bay outlet by 10,000 14C (11,470 cal) BP. Water levels were generally low between 10,000 and 7500 14C (11,470 and 8300 cal) BP and may have risen several tens of metres for short periods due to overflow of meltwater from upstream subglacial reservoirs or from glacial lakes impounded by residual ice in the Hudson Bay watershed.

About 8000 14C (8890 cal) BP glacial runoff bypassed the Great Lakes, and Huron basin waters descended into hydrologic closure under the influence of the early Holocene dry climate. With increasing precipitation and water supply about 7500 14C (8300 cal) BP the Huron water body again overflowed its North Bay outlet. Differential isostatic uplift (fastest to the north-northeast) raised this outlet and lake level relative to the rest of the basin. The lake finally overflowed southern outlets at Chicago and Port Huron-Sarnia by 5000 14C (5760 cal) BP (during the Nipissing highstand). Enhanced erosion of the latter outlet and continued differential uplift of the basin led to the present configuration of Lake Huron and Georgian Bay.
The late quaternary oxygen-isotope composition of Southern Lake Huron
Authors: Macdonald Rebecca A. , Longstaffe Fred J.
Published: June 2008

Meltwater events that affected Lake Huron during the last ∼ 12,000 years using the oxygen-isotope records provided by ostracodes have been identified. Three sediment cores were collected from Lake Huron; two from the Goderich Basin and one from the southern Manitoulin Basin. At certain times, these regions were isolated from each other and from other basins in the lake. The oxygen-isotope values obtained for the ostracodes indicate large variations in the composition of lake water, as has been reported elsewhere in Lake Huron. Lake Huron was inundated at least three times by water with very low δ18O values (∼ −20 versus ∼ −7.5% for modern Lake Huron water). This low-18O water originated from the retreating Laurentide ice sheet. It was likely derived from proglacial Lake Agassiz, and may have been released during very short intervals of time. Other periods were characterized by lake water with much higher δ18O values, reaching a maximum of −6.1%. Overall, the oxygen-isotope compositions of early Lake Huron water and its precursors are characterized by extreme variations, which arose both from changing sources and regional climate change.
Application of a Nested-grid hydrodynamic model for circulation and thermal structure in the coastal boundary layer of Lake Huron
Authors: Rao Yerubandi R. , Sheng Jinyu
Published: June 2008

A nested-grid hydrodynamic modeling system is used to study circulation and temperature distributions in Lake Huron and adjacent areas. This nested system is based on a three-dimensional, primitive-equation z-level ocean model. The nested system consists of two sub-components: a coarse-resolution outer model covering Lake Huron and Georgian Bay with a horizontal resolution of roughly 2.5 km, and a fine-resolution inner model covering eastern Lake Huron and northwestern Georgian Bay with a horizontal resolution of roughly 900 m. The inner model produced reasonably well the three-dimensional flow and thermal structure over the coastal boundary layer close to the eastern shore of the lake.
Influence of environmental conditions on late-summer cyanobacterial abundance in Saginaw Bay, Lake Huron
Authors: Millie D. F. , Fahnenstiel G. L. , Dyble J. , Pigg R. , Rediske R. , Klarer D. M. , Litaker R. W. , Tester P. A.
Published: June 2008

The relationships among environmental conditions and phytoplankton assemblages were characterized during late summer (2003-2005) in Saginaw Bay, Lake Huron. Differences among sampling stations, arising primarily from spatial disparities in water-column optical properties and nutrient availability, were evident. Cyanobacteria and diatoms dominated phytoplankton assemblages, with the greatest total chlorophyll a concentrations occurring at the innermost portions of the Bay. Microcystis abundance was greatest in the Bay's upper reaches and decreased with increasing distance from the mouth of the Saginaw River. A suite of variables, indicative of annually-distinct meteorological and hydrological conditions and phosphorus-laden inflows, were identified to (collectively) best ‘group’ stations in a manner consistent with that of phylogenetic-group chlorophyll a concentrations and cyanobacterial biovolumes. However, a great deal of variability between abiotic and biotic patterns remained unexplained and several abiotic variables singularly corresponded with Microcystis abundance. Taken together, it appears that multiple environmental conditions (including annual/episodic meteorological patterns, seasonal/intermittent riverine inflows, annual phosphorus loading, etc.) interact with taxon-specific physiological traits to holistically influence late-summer phytoplankton abundance throughout inner Saginaw Bay.
Domestic wastewater treatment using tidal-flow cinder bed with Cyperus alternifolius
Authors: Chan S. Y. , Tsang Y. F. , Chua H.
Published: June 2008

A lab-scale vertical flow cinder bed was set up to treat domestic wastewater. Cinder, which is a common coal waste from electricity generation, was used as the filter medium in the six vertical flow column beds in this study. Three of the six columns were planted with umbrella grass (Cyperus alternifolius) to mimic a wetland system and to investigate the effects of plant on the pollutant removal efficiencies of the column bed systems. The six column beds were divided into three groups, operating with different durations of “wet” and “dry” periods. Group 2 column beds, with 4 hours “wet” periods and 4 hours “dry” periods, showed the highest carbonaceous removal. And similar ammonia nitrogen removal efficiencies were demonstrated in column beds of group 2 and in column beds of group 3 (6 hours “wet” periods and 2 hours “dry” periods). Phosphorus removal efficiencies were not significantly different in all groups of column bed. No significant differences in pollutant removal were observed between planted and unplanted column beds in this study (p > 0.05).
Advanced qualification methodology for actively cooled plasma facing components
Authors: A. Durocher  , F. Escourbiac  , A. Grosman  , J. Boscary  , M. Merola  , F. Cismondi  , X. Courtois  , J.L. Farjon  , M. Missirlian  , J. Schlosser  , R. Tivey
Published: June 2008

The address for affiliation 1 is incorrect. The correct address should be Association Euratom-CEA, CEA/DSM/DRFC, F-13108, Saint Paul lez Durance.
ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth
Authors: Lambert Brian W. , Terwilliger Joseph D. , Weiss Kenneth M.
Published: June 2008

Many important problems in biology involve complex traits affected by multiple coding or regulatory parts of the genome. How well the underlying genetic architecture can be inferred by statistical methods such as mapping and association studies are active research areas. ForSim is a flexible forward evolutionary simulation tool for exploring the consequences of evolution by phenotype, whereby demographic, chance, behavioral and selective effects mold genetic architecture. Simulation is useful for exploring these issues as well as the choice of study design inferential methods.

Contact:  bwl1@psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Removing bias from solvent atoms in electron density maps
Authors: Brown Eric N.
Published: June 2008

Atomic structures of proteins determinedviaprotein crystallography contain numerous solvent atoms. The experimental data for the determination of a water molecule's O-atom position is often a small contained blob of unidentified electron density. Unfortunately, the nature of crystallographic refinement lets poorly placed solvent atoms bias the future refined positions of all atoms in the crystal structure. This research article presents the technique of omit-maps applied to remove the bias introduced by poorly determined solvent atoms, enabling the identification of incorrectly placed water molecules in partially refined crystal structures. A total of 160 protein crystal structures with 45 912 distinct water molecules were processed using this technique. Most of the water molecules in the deposited structures were well justified. However, a few of the solvent atoms in this test data set changed appreciably in position, displacement parameter or electron density when fitted to the solvent omit-map, raising questions about how much experimental support exists for these solvent atoms.
Crystal structure of a carbonyl reductase from Candida parapsilosis with anti‐Prelog stereospecificity
Authors: Zhang Rongzhen , Zhu Guangyu , Zhang Wenchi , Cao Sheng , Ou Xianjin , Li Xuemei , Bartlam Mark , Xu Yan , Zhang Xuejun C. , Rao Zihe
Published: June 2008

A novel short‐chain (S)‐1‐phenyl‐1,2‐ethanediol dehydrogenase (SCR) from Candida parapsilosis exhibits coenzyme specificity for NADPH over NADH. It catalyzes an anti‐Prelog type reaction to reduce 2‐hydroxyacetophenone into (S)‐1‐phenyl‐1,2‐ethanediol. The coding gene was overexpressed in Escherichia coli and the purified protein was crystallized. The crystal structure of the apo‐form was solved to 2.7 Å resolution. This protein forms a homo‐tetramer with a broken 2‐2‐2 symmetry. The overall fold of each SCR subunit is similar to that of the known structures of other homologous alcohol dehydrogenases, although the latter usually form tetramers with perfect 2‐2‐2 symmetries. Additionally, in the apo‐SCR structure, the entrance of the NADPH pocket is blocked by a surface loop. In order to understand the structure–function relationship of SCR, we carried out a number of mutagenesis–enzymatic analyses based on the new structural information. First, mutations of the putative catalytic Ser‐Tyr‐Lys triad confirmed their functional role. Second, truncation of an N‐terminal 31‐residue peptide indicated its role in oligomerization, but not in catalytic activity. Similarly, a V270D point mutation rendered the SCR as a dimer, rather than a tetramer, without affecting the enzymatic activity. Moreover, the S67D/H68D double‐point mutation inside the coenzyme‐binding pocket resulted in a nearly 10‐fold increase and a 20‐fold decrease in the kcat/KM value when NADH and NADPH were used as cofactors, respectively, with kcat remaining essentially the same. This latter result provides a new example of a protein engineering approach to modify the coenzyme specificity in SCR and short‐chain dehydrogenases/reductases in general.
WtsE, an AvrE‐family type III effector protein of Pantoea stewartii subsp. stewartii, causes cell death in non‐host plants
Authors: HAM JONG HYUN , MAJERCZAK DORIS , EWERT SOPHIE , SREEREKHA MYSORE‐VENKATARAU , MACKEY DAVID , COPLIN DAVID
Published: June 2008

Pantoea stewartii subsp. stewartii (Pnss) causes Stewart's bacterial wilt of sweet corn and leaf blight of maize. The pathogenicity of Pnss depends on synthesis of extracellular polysaccharide and an Hrp type III secretion system. WtsE, a type III secreted effector protein, is essential for the virulence of Pnss on corn. It belongs to the AvrE family of effectors, which includes DspA/E from Erwinia amylovora and AvrE1 from Pseudomonas syringae. Previously, WtsE was shown to cause disease‐associated cell death in its host plant, sweet corn. Here, we examine the biological activity of WtsE in several non‐host plants. WtsE induced cell death in Nicotiana benthamiana, tobacco, beet and Arabidopsis thaliana when it was transiently produced in plant cells following agroinfiltration or translocated into plant cells from Pnss, Escherichia coli or Pseudomonas syringae pv. phaseolicola (Pph). WtsE‐induced cell death in N. benthamiana, tobacco and beet resembled a hypersensitive response and in N. benthamiana it was delayed by cycloheximide. Interestingly, WtsE strongly promoted the growth of Pnss in N. benthamiana prior to the onset of cell death. Deletion derivatives of WtsE that failed to induce cell death in N. benthamiana and tobacco also did not complement wtsE mutants of Pnss for virulence in sweet corn, indicating a correlation between the two activities. WtsE also induced cell death in A. thaliana, where it suppressed basal defences induced by Pph. Thus, WtsE has growth‐promoting, defence‐suppressing and cell death‐inducing activities in non‐host plants. Expression of WtsE also prevented the growth of yeast, possibly due to an innate toxicity to eukaryotic cells.
Estimation of the number of SNP genetic markers required for parentage verification
Authors: Baruch E. , Weller J. I.
Published: June 2008

Formulae were developed to compute exclusion probabilities for parentage confirmation for any number of diallelic markers under the assumption that the minor allele frequency (MAF) varied among markers, but has a uniform distribution. Three scenarios were analysed: a progeny with (1) a single putative parent; (2) two putative parents; and (3) one actual parent and one putative parent. Exclusion probabilities were computed for minimum values for the MAFs of 0.1, 0.2 and 0.3, and required either one or at least two conflicts for exclusion. The numbers of markers required to obtain 99% exclusion probabilities based on a single conflict for the three minimum MAFs were 54, 45 and 39 for scenario 1; 17, 16 and 15 for scenario 2; and 28, 25 and 24 for scenario 3. The requirement of at least two conflicts for exclusion increased the number of markers required by approximately 45% for all three scenarios and all three minimum MAFs. The results obtained by the analytical formulae were very close to results obtained by simulation and to values in the literature for specific marker sets.
Cisapride and ventricular arrhythmia
Authors: Hennessy Sean , Leonard Charles E. , Newcomb Craig , Kimmel Stephen E. , Bilker Warren B.
Published: June 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Case reports have linked cisapride to ventricular arrhythmia and sudden cardiac death.

• However, two prior epidemiological studies have failed to show an association between cisapride and serious arrhythmia.

WHAT THIS STUDY ADDS

• Overall, cisapride was associated with a doubling to tripling of the risk of hospitalization for sudden cardiac death and ventricular arrhythmia, and a near eightfold risk in the initial prescription period.

• Although potentially arrhythmogenic CYP3A4 inhibitors were associated with an increased risk in cisapride users, this appears to be due to a direct effect of the drugs themselves rather than an interaction with cisapride.

AIMS

We aimed to examine the association between cisapride and ventricular arrhythmia, and examine the relationship to dose and CYP3A4 inhibitors.

METHODS

A nested case–control study was conducted in Medicaid beneficiaries exposed to cisapride, metoclopramide or a proton pump inhibitor (PPI) from 1999 to 2000. Cases were hospitalized with a principal International Classification of Diseases‐9 code indicating sudden cardiac death or ventricular arrhythmia. Controls had at least as much event‐free person time following the study prescription as its matched case.

RESULTS

A total of 145 cases and 7250 controls were identified. The unadjusted rate ratio for cisapride vs. PPIs was 1.49 (95% confidence interval 0.96, 2.25). The adjusted odds ratio (OR) for cisapride vs. PPIs was 2.10 (1.34, 3.28). Excluding persons in managed care, the adjusted OR for cisapride was 2.92 (1.55, 5.49). In the initial prescription period, the adjusted OR for cisapride vs. PPIs was 7.85 (1.95, 31.60). Non‐arrhythmogenic CYP3A4 inhibitors were not associated with an increased risk in users of cisapride or PPI inhibitors. The OR for potentially arrhythmogenic CYP3A4 inhibitors was 3.79 (1.76, 8.15) in cisapride users and 3.47 (2.06, 5.83) in PPI users.

CONCLUSIONS

Cisapride was associated with a doubling to tripling of the risk of hospitalization for ventricular arrhythmia, and a nearly eightfold risk in the initial prescription period. Although use of potentially arrhythmogenic CYP3A4 inhibitors was associated with an increased risk, this appears to be due to a direct effect of the drugs themselves rather than an interaction with cisapride.
An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase
Authors: Kohlmann Alexander , Kipps Thomas J. , Rassenti Laura Z. , Downing James R. , Shurtleff Sheila A. , Mills Ken I. , Gilkes Amanda F. , Hofmann Wolf‐Karsten , Basso Giuseppe , Dell’Orto Marta Campo , Foà Robin , Chiaretti Sabina , De Vos John , Rauhut Sonja , Papenhausen Peter R. , Hernández Jesus M. , Lumbreras Eva , Yeoh Allen E. , Koay Evelyn S. , Li Rachel , Liu Wei‐min , Williams Paul M. , Wieczorek Lothar , Haferlach Torsten
Published: June 2008

Gene expression profiling has the potential to enhance current methods for the diagnosis of haematological malignancies. Here, we present data on 204 analyses from an international standardization programme that was conducted in 11 laboratories as a prephase to the Microarray Innovations in LEukemia (MILE) study. Each laboratory prepared two cell line samples, together with three replicate leukaemia patient lysates in two distinct stages: (i) a 5‐d course of protocol training, and (ii) independent proficiency testing. Unsupervised, supervised, and r2 correlation analyses demonstrated that microarray analysis can be performed with remarkably high intra‐laboratory reproducibility and with comparable quality and reliability.
The role of NF‐κB in lymphoid malignancies
Authors: Packham Graham
Published: June 2008

Nuclear Factor kappaB (NF‐κB) transcription factors are central regulators of lymphocyte proliferation, survival and development. Although normally subject to tight control, constitutive activation of NF‐κB promotes inappropriate lymphocyte survival and proliferation, and is recognised as key pathological feature in various lymphoid malignancies. Inhibition of NF‐κB may be an attractive therapeutic approach in these diseases. This review focuses on the mechanisms and functional consequences of NF‐κB activation in lymphoid malignancies and potential therapeutic strategies for inhibition of NF‐κB.
The role of colonic metabolism in lactose intolerance
Authors: He T. , Venema K. , Priebe M. G. , Welling G. W. , Brummer R.‐J. M. , Vonk R. J.
Published: June 2008

Lactose maldigestion and intolerance affect a large part of the world population. The underlying factors of lactose intolerance are not fully understood. In this review, the role of colonic metabolism is discussed, i.e. fermentation of lactose by the colonic microbiota, colonic processing of the fermentation metabolites and how these processes would play a role in the pathophysiology of lactose intolerance. We suggest that the balance between the removal and production rate of osmotic–active components (lactose, and intermediate metabolites, e.g. lactate, succinate, etc.) in the colon is a key factor in the development of symptoms. The involvement of the colon may provide the basis for designing new targeted strategies for dietary and clinical management of lactose intolerance.
Soil microbial activity along an arctic‐alpine altitudinal gradient from a seasonal perspective
Authors: Löffler U. C. M. , Cypionka H. , Löffler J.
Published: June 2008

The knowledge on dynamics of soil microbial activity and its correlation to climate and vegetation is still poor but essential for predicting climatic changes scenarios. Seasonal dynamics of soil microbial activity and cell counts were studied along an arctic‐alpine altitudinal gradient. The gradient comprised 12 ridges from 1000 to 1600 m altitude. Soil samples were collected during March, May, July and September 2005. The effect of temperature, snow depth and vegetation, all of which changed with altitude, on soil microbial activity and bacterial cell counts was analysed. The potential activities of phosphatase and chitinase were determined using fluorescent 4‐methylumbelliferyl labelled analogues. Total and live bacterial cell counts were determined by live‐dead‐staining. We detected marked differences in soil microbial variables along the altitudinal gradient, forming three major clusters: a low alpine belt, a middle alpine belt, and an intermediate transition zone. Our results demonstrated that more frequent occurrence of shrubs and bryophytes would also increase microbial activity. Furthermore, we detected a clear relation (R2 = 0.6; P < 0.02) between high soil temperatures and greater soil microbial activity during summer. As higher temperatures are predicted to promote shrubs and higher humidity to promote bryophytes we expect microbial activity in dry heath tundra soils will increase with anticipated warmer, and in the case of Scandinavia, more humid climates. We did not find winter microbial activity to be less at snow‐free sites than at sites covered by snow up to depths of 30 cm; hence, possible future decreases in snow depth will not result in reduced winter microbial activity. We demonstrate that shrubs support winter microbial activity not only by trapping snow but also directly by increasing the amount of organic carbon.
Efficacy of citric acid against Listeria monocytogenes attached to poultry skin during refrigerated storage
Authors: González‐Fandos Elena , Herrera Bárbara , Maya Naiara
Published: June 2008

The aim of this study was to evaluate the effect of citric acid washing on the growth of Listeria monocytogenes on poultry legs stored at 4 °C for 8 days. Fresh inoculated chicken legs were dipped into either a 0.052, 0.104 or 0.156 m citric acid solution for 5 min or distilled water (control). Surface pH values, sensorial characteristics and L. monocytogenes, mesophiles and psychrotrophs counts were evaluated. Legs washed with 0.156 m citric acid for 5 min showed a significant (P < 0.05) inhibitory effect on L. monocytogenes compared with control legs, being about 1.55 log units lower in the first ones than in control legs after 1 day of storage. Treatments with 0.156 m citric acid reduced bacterial growth and preserved reasonable sensorial quality after storage at 4 °C for 8 days.
Microwave heat treatment of leek: drying kinetic and effective moisture diffusivity
Authors: Dadali Gökçe , Özbek Belma
Published: June 2008

The effect of microwave drying technique on moisture ratio, drying time and effective moisture diffusivity of white and green parts of leek (Allium porrum) were investigated. By increasing the sample amount (100–300 g) at constant microwave output power of 180 W, the drying time increased from 52 to 130 min and increased from 55 to 135 min for white and green parts of leek, respectively. Effective moisture diffusivity values for white and green parts of leek ranged from 0.618 × 10−10 to 2.128 × 10−10 m2.s−1 and 0.256 × 10−10 to 0.611 × 10−10 m2 s−1, respectively. Among the models proposed, Midilli et al. model gave a better fit for all drying conditions applied. The activation energy for microwave drying of white and green parts of leek was calculated using an exponential expression based on Arrhenius equation; found as 0.9530 and 1.2045 W g−1, respectively. The dependence of drying rate constant on effective moisture diffusivity gave a linear relationship.
Functional properties of hydrolysates from Phaseolus lunatus seeds
Authors: Betancur‐Ancona David , Martínez‐Rosado Rogelio , Corona‐Cruz Alma , Castellanos‐Ruelas Arturo , Jaramillo‐Flores Ma Eugenia , Chel‐Guerrero Luis
Published: June 2008

Use of low degree of hydrolysis (DH < 10%) with enzymatic treatment can produce protein hydrolysates with functional properties superior to the raw material. Suspensions of Phaseolus lunatus protein isolate (PPI) were treated with one of two commercial enzymes (Alcalase or Flavourzyme) at 50 °C and pH 8.0. DH with Alcalase was greater than Flavourzyme at 5 or 15 min of reaction. Alcalase‐prepared hydrolysates had more peptides than those prepared with Flavourzyme. All the hydrolysates had higher solubility than the PPI, the highest being for the Alcalase‐prepared hydrolysate at 15 min reaction time. Overall, the Alcalase‐prepared hydrolysates had better solubility characteristics, whereas the Flavourzyme‐prepared hydrolysates had better film properties (maximum emulsifying capacity and the highest foam formation values). This is probably because of the greater ease of movement toward the interface as shown by their high surface hydrophobicity values. The Alcalase‐prepared hydrolysates had generally low or nonexistent film properties.
Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation
Authors: MORGAN MATTHEW J. , HUNTER DAVID , PIETSCH ROD , OSBORNE WILLIAM , KEOGH J. SCOTT
Published: June 2008

The iconic and brightly coloured Australian northern corroboree frog, Pseudophryne pengilleyi, and the southern corroboree frog, Pseudophryne corroboree are critically endangered and may be extinct in the wild within 3 years. We have assembled samples that cover the current range of both species and applied hypervariable microsatellite markers and mitochondrial DNA sequences to assess the levels and patterns of genetic variation. The four loci used in the study were highly variable, the total number of alleles observed ranged from 13 to 30 and the average number of alleles per locus was 19. Expected heterozygosity of the four microsatellite loci across all populations was high and varied between 0.830 and 0.935. Bayesian clustering analyses in structure strongly supported four genetically distinct populations, which correspond exactly to the four main allopatric geographical regions in which the frogs are currently found. Individual analyses performed on the separate regions showed that breeding sites within these four regions could not be separated into distinct populations. Twelve mtND2 haplotypes were identified from 66 individuals from throughout the four geographical regions. A statistical parsimony network of mtDNA haplotypes shows two distinct groups, which correspond to the two species of corroboree frog, but with most of the haplotype diversity distributed in P. pengilleyi. These results demonstrate an unexpectedly high level of genetic diversity in both species. Our data have important implications for how the genetic diversity is managed in the future. The four evolutionarily significant units must be protected and maintained in captive breeding programmes for as long as it is possible to do.
Habitat‐specific natural selection at a flowering‐time QTL is a main driver of local adaptation in two wild barley populations
Authors: VERHOEVEN K. J. F. , POORTER H. , NEVO E. , BIERE A.
Published: June 2008

Understanding the genetic basis of local adaptation requires insight in the fitness effects of individual loci under natural field conditions. While rapid progress is made in the search for genes that control differences between plant populations, it is typically unknown whether the genes under study are in fact key targets of habitat‐specific natural selection. Using a quantitative trait loci (QTL) approach, we show that a QTL associated with flowering‐time variation between two locally adapted wild barley populations is an important determinant of fitness in one, but not in the other population's native habitat. The QTL mapped to the same position as a habitat‐specific QTL for field fitness that affected plant reproductive output in only one of the parental habitats, indicating that the genomic region is under differential selection between the native habitats. Consistent with the QTL results, phenotypic selection of flowering time differed between the two environments, whereas other traits (growth rate and seed weight) were under selection but experienced no habitat‐specific differential selection. This implies the flowering‐time QTL as a driver of adaptive population divergence. Our results from phenotypic selection and QTL analysis are consistent with local adaptation without genetic trade‐offs in performance across environments, i.e. without alleles or traits having opposing fitness effects in contrasting environments.