bluuebunny/crossref_metadata_2025 huggingface dataset:
Species‐dependent stereoselective drug binding to albumin: A circular dichroism study
Authors: Pistolozzi Marco , Bertucci Carlo
Published: January 2008

Drug binding to albumins from different mammalian species was investigated to disclose evidence of species‐dependent stereoselectivity in drug‐binding processes and affinities. This aspect is important for evaluating the reliability of extrapolating distribution data among species. The circular dichroism (CD) signal induced by drug binding to the albumins [human serum albumin (HSA), bovine serum albumin (BSA), rat serum albumin (RSA), and dog serum albumin (DSA)] were measured and analyzed. The binding of selected drugs and metabolites to HSA significantly differed from the binding to the other albumins in terms of affinity and conformation of the bound ligands. In particular, phenylbutazone, a marker of site one on HSA, showed a higher affinity for binding to BSA with respect to RSA, HSA, and DSA, respectively. In the case of diazepam, a marker of site two on HSA, the affinity decreased in order from HSA to DSA, RSA, and BSA. The induced CD spectra were similar in terms of energy and band signs, suggesting almost the same conformation for the bound drug to the different albumins. Stereoselectivity was high for the binding of ketoprofen to HSA and RSA. A different sign was observed for the CD spectra induced by the drug to the two albumins because of the prevalence of a different conformation of the bound drug. Interestingly, the same induced CD spectra were obtained using either the racemic form or the (S)‐enantiomer. Finally, significant differences were observed in the affinity of bilirubin, being highest for BSA, then decreasing for RSA, HSA, and DSA. A more complex conformational equilibrium was observed for bound bilirubin. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Enantioselective HPLC of potentially CNS‐active acidic amino acids with a cinchona carbamate based chiral stationary phase
Authors: Sardella Roccaldo , Lämmerhofer Michael , Natalini Benedetto , Lindner Wolfgang
Published: January 2008

A tert‐butylcarbamoylquinine‐based chiral stationary phase (Chiralpak QN‐AX) has been employed for the enantiomer separation of underivatized chiral acidic amino acids, viz. 4‐carboxyphenylalanine (4‐CPHE), 1‐aminoindan‐1,5‐dicarboxylic acid (AIDA), 2‐(5‐carboxy‐3‐methyl‐2‐thienyl)glycine (3‐MATIDA), 2‐(4‐carboxy‐5‐methyl‐2‐thienyl)glycine (5‐MATIDA), and 2‐(2′‐carboxy‐3′‐phenylcyclopropyl)glycine (PCCG). Some of the acidic amino acids have potential activity on the central nervous system and are thus of great interest. A stereoselective HPLC method that allows the baseline resolution of all the five test solutes has been developed. For that purpose the mobile phase composition (pH, organic modifier, and type) and flow rate were optimized. The final method makes use of mild elution conditions, namely methanol – 0.8 M ammonium acetate buffer (97.5:2.5; v/v) pH 5.5 which are also compatible with mass spectrometric detection. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Neuroprotection of hypothermia against neuronal death in rat hippocampus through inhibiting the increased assembly of GluR6‐PSD95‐MLK3 signaling module induced by cerebral ischemia/reperfusion
Authors: Hu Wei‐Wei , Du Yang , Li Chong , Song Yuan‐Jian , Zhang Guang‐Yi
Published: January 2008

Kainate receptor containing GluR6 subunit (KAR) is involved in the neuronal cell death induced by cerebral ischemia/reperfusion (I/R). Hypothermia is an effective neuroprotectant in brain ischemia, whereas the neuroprotective mechanisms have not been clearly established. The present study was set out to examine whether hypothermia would cause the alternation of the assembly of the GluR6‐PSD95‐MLK3 signaling module and the activation of c‐Jun N‐terminal kinase (JNK) pathway through KAR. Hypothermia (32°C) was induced 10 min before ischemia and was maintained for 3 h after ischemia. Our results indicated that hypothermia could inhibit the assembly of GluR6‐PSD95‐MLK3 signaling module and suppressed the activation of MLK3, MKK4/7, and JNK3. The inhibition of JNK3 activation by hypothermia diminished the phosphorylation of the transcription factor c‐Jun and downregulated FasL expression in hippocampal CA1. Meanwhile, the inhibition of JNK3 activation by hypothermia attenuated bax translocation, the release of cytochrome c, and the activation of caspase‐3 in CA1 subfields. Both GluR6 antagonist NS102 and GluR6 antisense oligodeoxynucleotides partly blocked the aforementioned effects of hypothermia, which was further confirmed by histology. Taken together, our results strongly suggest that hypothermia decreased the increased assembly of the GluR6‐PSD95‐MLK3 signaling module and the activation of JNK pathway induced by I/R through KAR, which gave a new insight into the ischemic therapy. © 2008 Wiley‐Liss, Inc.
Atoms‐in‐molecules analysis for planewave DFT calculations—A numerical approach on a successively interpolated charge density grid
Authors: Yim Wai‐Leung , Klüner Thorsten
Published: January 2008

We used a successive charge interpolation scheme and Ridders method for differentiation, to acquire accurate charge densities and their higher derivatives in electronic structure calculations. This enables us to search bond critical points using arbitrary charge density grids. We applied the planewave‐DFT code, VASP, to generate the charge density of selected benchmark molecules. The properties of bond critical points are in good agreement with those obtained by complementary implementations. We validated our GRID implementation by performing electronic structure calculations using the Gaussian 03 program package and various tools for analysis of the charge density provided by the AIMPAC package. In particular, we carefully investigate the influence of effective core potentials on the location of bond critical points, especially for a short chemical bond, which is crucial in the present pseudopotential‐based planewave DFT calculations. We expect our generic implementation will not only be useful for the analysis of chemical bonding in molecules, but will particularly provide a microscopic understanding of extended systems including periodic boundary conditions. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Gender and local floodplain management institutions: a case study from Bangladesh
Authors: Sultana Parvin , Thompson Paul
Published: January 2008

Floodplain wetlands are the major common pool natural resources in Bangladesh. Men do most of the fishing, but women collect aquatic plants and snails. A women‐only, a men‐only, and a mixed community based organisation (CBO) are compared, each of which manages a seasonal wetland. The CBOs involving women are in Hindu communities where more women use aquatic resources and belong to other local institutions. In the oldest of these CBOs, women have gradually increased their role as community recognition of their success has grown. In the Muslim community few women collect aquatic resources, and they have no role in the CBO. Community compliance was higher where both men and women played an active role in the process. Copyright © 2008 John Wiley & Sons, Ltd.
Electron Microscopy and Microanalysis of the Fiber–Matrix Interface in Monolithic Silicone Carbide‐Based Ceramic Composite Material for Use in a Fusion Reactor Application
Authors: Toplisek Tea , Drazic Goran , Novak Sasa , Kobe Spomenka
Published: January 2008

A composite material made from continuous monolithic silicone carbide (SiC) fibers and a SiC‐based matrix (SiCf/SiC), was prepared using a novel technique, i.e. adapted dip coating and infiltration of SiC fibers with a water suspension containing SiC particles and a sintering additive. This kind of material could be used in the first‐wall blanket of a future fusion reactor. Using magnetron sputtering, the SiC fibers were coated with various thin layers (TiC, CrN, CrC, WC, DLC—diamond‐like carbon) of the interface material by physical vapor deposition (PVD). Using scanning and transmission electron microscopy and microanalysis, detailed microstructural studies of the fiber‐matrix interface were performed. Both samples, with coated and uncoated fibers, were examined under a load. The microcracks introduced by the Vickers indenter continued their path through the fibers, and thus caused the failure of the composite material, in the case of the uncoated fibers or deviated from their primary direction at the fiber‐matrix interface in the case of the coated fibers. SCANNING 30: 35–40, 2008. © 2008 Wiley Periodicals, Inc.
Environmental citizenship and sustainable development: the case of waste facility siting in Taiwan
Authors: Fan Mei‐Fang
Published: January 2008

This paper examines how issues of environmental citizenship play out in the context of an industrial waste facility siting controversy in Taipei, Taiwan, and the implications of this complex predicament for justice and sustainable development generally. It shows the ways in which local activists perceive the adverse effects of a development project that generates industrial waste and incinerator ash in their hometown. Local activists feel excluded from decision‐making and frustrated by the lack of recognition by authorities. They complain that their local, contextualized knowledge and experiences are ignored. Local activists are concerned about ecological devastation and feel responsible for future generations. Instead of a NIMBY protest of selfish residents, local activists imagine themselves as active citizens fighting for justice and sustainability on a scale beyond their neighborhood. The case highlights the needs for institutional transparency, the recognition of multiple ways of knowing and new conceptions of the good life. Copyright © 2008 John Wiley & Sons, Ltd and ERP Environment.
Estimating the empirical Lorenz curve and Gini coefficient in the presence of error with nested data
Authors: Moskowitz Chaya S. , Seshan Venkatraman E. , Riedel Elyn R. , Begg Colin B.
Published: January 2008

The Lorenz curve is a graphical tool that is widely used to characterize the concentration of a measure in a population, such as wealth. It is frequently the case that the measure of interest used to rank experimental units when estimating the empirical Lorenz curve, and the corresponding Gini coefficient, is subject to random error. This error can result in an incorrect ranking of experimental units which inevitably leads to a curve that exaggerates the degree of concentration (variation) in the population. We consider a specific data configuration with a hierarchical structure where multiple observations are aggregated within experimental units to form the outcome whose distribution is of interest. Within this context, we explore this bias and discuss several widely available statistical methods that have the potential to reduce or remove the bias in the empirical Lorenz curve. The properties of these methods are examined and compared in a simulation study. This work is motivated by a health outcomes application that seeks to assess the concentration of black patient visits among primary care physicians. The methods are illustrated on data from this study. Copyright © 2008 John Wiley & Sons, Ltd.
Midgut volvulus with hemorrhagic ascites: a rare cause of fetal anemia
Authors: Noreldeen S. A. , Hodgett S. G. , Venkat‐Raman N.
Published: January 2008

Fetal intestinal volvulus is a rare life‐threatening condition usually manifesting after birth. It appears on prenatal ultrasound imaging as a twisting of the bowel loops around the mesenteric artery, leading to mechanical obstruction and ischemic necrosis of the bowel. Vascular compromise can result in bowel infarction and eventual perforation of the necrotic bowel, with the development of hemorrhagic fetal ascites and fetal anemia. We report a case of intrauterine midgut volvulus, suspected when ultrasound imaging revealed dilated bowel loops at 31 weeks' gestation, with fetal anemia also suspected on measurement of increased middle cerebral artery peak systolic velocity by Doppler ultrasound examination. Volvulus should be considered in the differential diagnosis when ultrasound imaging demonstrates dilated loops of bowel, especially in association with fetal ascites. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
An evaluation of CHD‐Specific primer sets for sex typing of birds from feathers
Authors: Ong Alan H.K. , Vellayan Subramaniam
Published: January 2008

The amplification of the highly conserved chromo‐helicase‐DNA binding region found in both the Z and W chromosome was evaluated with three sets of primers (P8/P2, 1237L/1272H and 2550F/2718R). DNA extracted from feathers through a simple boiling method was used to address its reliability in generating the sex‐linked bands. All the bird samples, including the seven bird families that have not been reported previously, were successfully amplified with the primer set 2550F/2718R. The resulting polymerase chain reaction products showed clearly resolved fragments on a conventional agarose gel electrophoresis with size differences ranging from 80 to 540 bp between the two respective ZW gene copies. Although the P8/P2 primer was not as effective under the same conditions, it was able to produce well‐resolved Z and W bands from bird species under the Antidea family, whereas the 2250F/2718R primer set only produced a single amplified fragment of a different size between the male and the female. Zoo Biol 27:62–69, 2008. © 2007 Wiley‐Liss, Inc.
Effects of immunocontraception on behavior in fallow deer (Dama dama)
Authors: Darhower Sarah E. , Maher Christine R.
Published: January 2008

Immunocontraceptives can control growth in wild and captive populations; however, in doing so, they should not disrupt species‐typical behavior patterns. The presence of treated females could disrupt social interactions in a population; yet, few studies have examined effects of immunocontraception on behavior. The goal of this project was to determine whether behavior in a fallow deer (Dama dama) population vaccinated with porcine anti‐zona pellucida (pZP)‐immunocontraceptives differed from behavior in a population of unvaccinated deer. We predicted that pZP‐treated females would spend a higher percentage of time exhibiting mating and dominance behavior than nontreated females, and that males interacting with pZP‐treated females would spend a higher percentage of time demonstrating mating and aggressive behavior than males interacting with nontreated females. We recorded activity budgets of males and females in two fallow deer populations, one pZP‐treated and the other untreated, before, during, and after rut. Females did not differ in time spent displaying mating or dominance behavior compared to nontreated females. Males coexisting with nontreated females spent more time exhibiting aggressive behavior during rut than males living with pZP‐treated females, but males did not differ in time spent in mating behavior. Thus, immunocontraception did not seem to affect behavior adversely. However, sample sizes, living conditions, and sex ratios may have affected the results. Given these limitations, future research is needed to confirm our findings. Zoo Biol 27:49–61, 2008. © 2007 Wiley‐Liss, Inc.
An investigation of the relationship between fecal and rumen bacterial concentrations in sheep
Authors: Neumann Laura M. , Dehority Burk A.
Published: January 2008

With no acceptable method for collecting fresh rumen fluid from zoo ruminants, it was proposed that fecal bacterial concentrations may be correlated with rumen bacteria. If so, fecal bacterial concentrations could be used to study both the effects of diet on rumen bacteria as well as rumen abnormalities. Total and cellulolytic bacterial concentrations were determined in whole rumen contents and feces of sheep using a most‐probable‐number (MPN) assay. In a Latin square design, four crossbred ewes were fed diets of 100% long or chopped orchardgrass hay (OH) and 60% ground or whole shelled corn plus 40% chopped OH. In a second trial, the sheep were fed a pelleted complete feed at varying levels of intake i.e., control at 2.0% of body weight and at 1.8, 1.6, and 1.2% of body weight. Higher total rumen bacterial concentrations (P<0.01) were found on the high concentrate diets as compared with the high forage diets. Grinding the corn also increased total bacterial concentrations (P<0.05). Fecal concentrations of total bacteria were higher (P<0.01) with the high concentrate diets. Chopping the forage decreased the concentration of fecal cellulolytic bacteria (P<0.05) but had no effect on their concentration in the rumen. An inverse linear relationship (P<0.01) was observed between total bacterial concentrations in the feces and diet intake. Although relationships were observed between the rumen and feces for total and cellulolytic bacterial concentrations, they were dependent on diet, particle size, and level of intake. Thus, fecal bacterial concentrations cannot be used to reliably predict rumen bacterial concentrations. Zoo Biol 27:100–108, 2008. © 2008 Wiley‐Liss, Inc.
Endoscopic Thyroidectomy by the Breast Approach: A Single Institution’s 9‐year Experience
Authors: Sasaki Akira , Nakajima Jun , Ikeda Kenichiro , Otsuka Koki , Koeda Keisuke , Wakabayashi Go
Published: January 2008

Background

The aim of this study was to evaluate the feasibility and cosmetic results of endoscopic thyroidectomy by the breast approach for patients with thyroid diseases.

Methods

From August 1998 to July 2007, 92 patients with benign thyroid diseases underwent endoscopic thyroidectomy at our institution. Of these patients, 54 underwent thyroid lobectomy for a thyroid nodule, and 38 selected subtotal thyroidectomy for Graves’ disease.

Results

Ninety of the 92 procedures were successfully completed endoscopically. Mean operative time for thyroid lobectomy and subtotal thyroidectomy was 121.1 min and 231.9 min, repectively. Postoperative complications included one wound infection, one transient and one permanent recurrent laryngeal nerve palsy, one transient hypocalcemia, and five hypertrophic scars in the right breast medial margin. At 84 months of follow‐up, one patient reported paresthesia in the anterior chest and one had experienced swallowing discomfort. Patient satisfaction was recorded as “satisfied,” “equivocal,” and “unsatisfied” in 54, 2, and 0 patients. Mean satisfaction score was 9.7, 9.5, 9.5, and 8.9 points in patients in their teens, 20s, 30s, and 40s, respectively, with an overall mean score of 9.3 points, showing more satisfaction in the young.

Conclusions

Endoscopic thyroidectomy by the breast approach for patients with thyroid diseases is an effective procedure that allows an excellent cosmetic result.
Adalimumab for the treatment of Crohn‐like colitis and enteritis in glycogen storage disease type Ib
Authors: Davis M. K. , Rufo P. A. , Polyak S. F. , Weinstein D. A.
Published: January 2008

Glycogen storage disease (GSD) type Ib is a congenital disorder of glycogen metabolism that is associated with neutropenia, neutrophil dysfunction, and an inflammatory bowel disease that mimics a Crohn phenotype. Gastrointestinal inflammation in GSD Ib has been successfully treated with 5‐aminosalicylic acid and granulocyte colony‐stimulating factor (G‐CSF). However, therapeutic options for patients not responding to traditional therapies have been limited owing to untoward effects of glucocorticoids and immunomodulators in this metabolic disorder. Adalimumab is a monoclonal antibody targeting tumour necrosis factor‐α that has shown promise for the treatment of patients with Crohn disease. Due to the limited options for treating GSD‐associated inflammatory bowel disease, use of adalimumab was attempted in a case unresponsive to aminosalicylate, G‐CSF, and antibiotic therapy. Significant clinical and histological improvement was observed in our patient, and the medication was well tolerated.
Taste sensitivity for monosodium glutamate and an increased liking of dietary protein
Authors: Luscombe-Marsh Natalie D. , Smeets Astrid J. P. G. , Westerterp-Plantenga Margriet S.
Published: January 2008

The aim of the present study was to determine individuals' taste threshold for monosodium glutamate (MSG) alone and in combination with inosine 5′-monophosphate (IMP-5) and to examine if this threshold was related to an increase in sensory properties (including pleasantness of taste) and/or to one's preference for dietary protein over carbohydrate and fat. Using the triangle tasting method, the taste threshold was determined for thirty-six women and twenty-four men. Thresholds varied from zero to infinite as determined using a clear soup with added MSG in the concentration range of 0·1 to 0·8 % (w/w) MSG. Subjects rated fourteen sensory properties of the soup and also their ‘liking’, ‘eating frequency’ and ‘preference’ of twenty-two common high-protein, high-carbohydrate and high-fat food items. The taste threshold (and therefore sensitivity) of MSG was lowered from 0·33 (sem 0·24) to 0·26 (sem 0·22) % MSG when 0·25 % (w/w) IMP-5 was added. None of the sensory properties assessed was associated with the taste threshold of MSG ± 0·25 % IMP-5 in the overall study population. However, the taste descriptor ‘meatiness’ was associated with the threshold data for individuals who could taste concentrations of ≤ 0·4 % MSG. ‘Liking’ and ‘preference’ scores for protein were found to be related to the threshold of MSG ± 0·25 % IMP-5. From this study population we conclude that the taste threshold of MSG in combination with IMP-5 does appear to predict one's ‘liking’ of as well as ‘preference’ for high-protein foods.
Recent theoretical progress in understanding coherent structures in edge and SOL turbulence
Authors: KRASHENINNIKOV S. I. , D'IPPOLITO D. A. , MYRA J. R.
Published: January 2008

In this paper we review some theoretical aspects of the dynamics of the mesoscale filaments extending along the magnetic field lines in the edge plasma, which are often called ‘blobs’. We start with a brief historical survey of experimental data and the main ideas on edge and SOL plasma transport, which finally evolved into the modern paradigm of convective very-intermittent cross-field edge plasma transport. We show that both extensive analytic treatments and numerical simulations demonstrate that plasma blobs with enhanced pressure can be convected coherently towards the wall. The mechanism of convection is related to an effective gravity force (e.g. owing to magnetic curvature effects), which causes plasma polarization and a corresponding E× B convection. The impacts of different effects (e.g. X-point magnetic geometry, plasma collisionality, plasma beta, etc.) on blob dynamics are considered. Theory and simulation predict, both for current tokamaks and for ITER, blob propagation speeds and cross-field sizes to be of the order of a few hundred meters per second and a centimeter, respectively, which are in reasonable agreement with available experimental data. Moreover, the concept of blobs as a fundamental entity of convective transport in the scrape-off layer provides explanations for observed outwards convective transport, intermittency and non-Gaussian statistics in edge plasmas, and enhanced wall recycling in both toroidal and linear machines.
Fish consumption is a safe solution to increase the intake of long-chainn-3 fatty acids
Authors: Sioen Isabelle , De Henauw Stefaan , Verbeke Wim , Verdonck Frederik , Willems Jan L , Van Camp John
Published: January 2008

Objectives

Dietary intake of long-chain (LC)n-3 PUFA in developed countries is low compared with recommendations. Fish is naturally rich in LCn-3 PUFA, but is also a dietary source of heavy metals and organic pollutants. We investigated whether the recommendation for LCn-3 PUFA could be reached through fish consumption, without exceeding the provisional tolerable weekly intake of methylmercury (MeHg) and the tolerable weekly intake (TWI) of dioxin-like compounds. Also, the contribution of margarines enriched with LCn-3 PUFA was assessed.

Design

Published nutrient and contaminant data were used in a probabilistic model to calculate the simultaneous nutrient and contaminant intake for different fish consumption scenarios.

Results

The Belgian recommendation for EPA + DHA (0·3 % of total energy intake) can be reached by consuming fatty fish a minimum of twice a week, or by varying between lean and fatty fish a minimum of three times a week. At this fish consumption level, MeHg intake is not an issue of toxicological concern. The intake of dioxin-like compounds approximates the TWI when consuming fatty fish more than twice a week, this being a potential toxicological risk because other food items also contribute to the weekly intake of dioxin-like compounds. Use of margarine enriched with LCn-3 PUFA can help to increase LCn-3 intake, on average by 159 mg/d.

Conclusions

Combination of regular fish consumption (twice a week) with important contribution of fatty fish species, in combination with regular consumption of margarine enriched with EPA + DHA, can be advised to achieve the recommendation for LCn-3 intake.
Abiotic formation of RNA-like oligomers by montmorillonite catalysis: part II
Authors: Ertem Gözen , Snellinger-O'Brien Ann M. , Ertem M. C. , Rogoff D. A. , Dworkin Jason P. , Johnston Murray V. , Hazen Robert M.
Published: January 2008

This work is an extension of our previous studies carried out to investigate the possible catalytic role of minerals in the abiotic synthesis of biologically important molecules. In the presence of montmorillonite, a member of the phyllosilicate group minerals that are abundant on Earth and identified on Mars, activated RNA monomers, namely 5′-phosphorimidazolides of nucleosides (ImpNs), undergo condensation reactions in aqueous electrolyte solution producing oligomers with similar structures to short RNA fragments. Analysis of the linear trimer isomers formed in the reaction of a mixture of activated adenosine and cytidine monomers (ImpA and ImpC, respectively) employing high-performance liquid chromatography, selective enzymatic hydrolysis and matrix-assisted laser desorption/ionization mass spectroscopy molecular weight measurements demonstrate that montmorillonite catalysis facilitates the formation of hetero-isomers containing 56% A- and 44% C-monomer incorporated in their structure. The results also show that 56% of the monomer units are linked together by RNA-like 3′, 5′-phosphodiester bonds. These results follow the same trend observed in our most recent work studying the reaction of activated adenosine and uridine monomers, and support Bernal's hypothesis proposing the possible catalytic role of minerals in the abiotic processes in the course of chemical evolution.
Nutritional management for enteric methane abatement: a review
Authors: Beauchemin K. A. , Kreuzer M. , O'Mara F. , McAllister T. A.
Published: January 2008

A variety of nutritional management strategies that reduce enteric methane (CH4) production are discussed. Strategies such as increasing the level of grain in the diet, inclusion of lipids and supplementation with ionophores (>24 ppm) are most likely to be implemented by farmers because there is a high probability that they reduce CH4 emissions in addition to improving production efficiency. Improved pasture management, replacing grass silage with maize silage and using legumes hold some promise for CH4 mitigation but as yet their impact is not sufficiently documented. Several new strategies including dietary supplementation with saponins and tannins, selection of yeast cultures and use of fibre-digesting enzymes may mitigate CH4, but these still require extensive research. Most of the studies on reductions in CH4 from ruminants due to diet management are short-term and focussed only on changes in enteric emissions. Future research must examine long-term sustainability of reductions in CH4 production and impacts on the entire farm greenhouse gas budget.
The methanogenic potential and C-isotope fractionation of different diet types represented by either C3 or C4 plants as evaluated in vitro and in dairy cows
Authors: Klevenhusen F. , Bernasconi S. M. , Kreuzer M. , Soliva C. R.
Published: January 2008

The methanogenic potential of two major feed production systems, grassland and arable land, was tested in vitro and in vivo. Diets were differentiated into C3 (grass, cereals) and C4 plants (maize) to determine whether C-isotope fractionation during methane formation differed between the C3 and C4 plant based diets. In the in vitro experiment, four diets consisting of hay, maize, wheat (the latter two straw and grain) and a 1 : 1 mixture of the maize and wheat diet were investigated using the Rusitec system (n = 4 per diet). In the in vivo experiment with 12 lactating cows, diets were basically similar, but barley was used instead of wheat and no maize–cereal mixture was tested (n = 4 per diet). Diets were always iso-energetic and iso-nitrogenous. Methane was either measured by gas chromatography from complete daily collections (in vitro) or by putting cows into respiratory chambers. In vitro, the methanogenic potential of the diets was similar. Methane related to apparently degraded neutral detergent fibre (NDF) was 50% lower in the hay than in the wheat diet, while the other diets ranged in between. The largest C-isotope fractionation between fermentation gases (αCO2 – CH4) was found in the wheat diet. In vivo, methane formation was highest with the barley diet followed by the hay and the maize diet (580, 461 and 453 L/day). Relating methane emission to dry matter intake reduced differences among diets (average 34 L/kg). On average, 118 L of methane were produced per kg digested NDF. Methane conversion rate was higher than the IPCC default value of 6.5% given for diets with less than 90% concentrate. No differences in the C-isotope fractionation were found in vivo. It was shown that forage-only diets, containing higher levels of fermentable fibre, do not necessarily have a higher methanogenic potential than mixed forage-concentrate diets.
Using the OVERSEER nutrient budget model to estimate on-farm greenhouse gas emissions
Authors: Wheeler D. M. , Ledgard S. F. , DeKlein C. A. M.
Published: January 2008

The OVERSEER nutrient budget model is a farm-scale nutrient reporting and greenhouse gas (GHG) emission accounting tool used extensively throughout New Zealand (NZ) by farmers, farm consultants and fertiliser representatives. The model is increasingly being used as a tool for implementing regional council resource management requirements to limit nitrogen (N) and phosphorus losses to waterways. NZ’s main dairy company, Fonterra, also requires dairy farmers to have a nutrient budget as part of the national Clean Streams Accord. This means that a high proportion of NZ farmers can obtain reports of their on-farm GHG emission profile. The GHG emission model is based on models and algorithms used for the NZ GHG national inventory, modified to include a wide range of on-farm management practices. The model estimates methane, nitrous oxide and carbon dioxide (CO2) emissions, and presents the results as CO2 equivalents. This paper describes the model and the benefits of combining nutrients budgets and GHG emissions into a single model. It also demonstrates the effects of management practices on a range of outputs, including N leaching and GHG emissions.
The effect of oils fed to sheep on methane production and digestion of ryegrass pasture
Authors: Cosgrove G. P. , Waghorn G. C. , Anderson C. B. , Peters J. S. , Smith A. , Molano G. , Deighton M.
Published: January 2008

Selecting ryegrass for higher concentrations of lipid to increase dietary energy density may increase the productivity of pasture-fed animals and reduce rumen methane emissions. A proof-of-concept study was undertaken to identify responses of sheep to increasing dietary lipid intake. Sheep housed in metabolism crates were fed fresh ryegrass at 120% of ad libitum intake for two 17-day periods with dry matter intake (DMI) and energy balance measured over the final 7 days and methane over five consecutive days at the end of each period. A blend of linseed and sunflower oils (3 : 1) were infused directly into the rumen of 8-month-old wether sheep (37 ± 1.7 kg [mean ± s.d.]; n = 2 per level) to provide 0% (control), 1.2%, 2.5%, 3.7%, 5.0% and 6.2% of DMI. Sheep were re-randomised among treatments for the second measurement period. Oils were infused over 2 h during each of the morning and afternoon feeding period at rates calculated to achieve the target addition. Measurements included DMI, energy intake and digestibility, enteric methane production and rumen volatile fatty acid (VFA) profiles. Sheep tolerated additional oil up to 5% of DMI, but when 6.2% was given, intakes declined and this treatment was discontinued. Up to 5% oil infusion did not affect methane production, DMI, energy digestibility or rumen VFA concentrations or proportions. The results suggest plant breeding to increase fatty acid content may benefit production provided total lipid did not exceed 9% of the DM, but methane production during digestion would be unaffected.
Fumaric acid supplements have no effect on methane emissions per unit of feed intake in wether lambs
Authors: Molano German , Knight T. W. , Clark H.
Published: January 2008

Recent reports suggest that supplementing the diet of ruminants with up to 10% fumaric acid (FA) can produce large reductions in methane (CH4) emissions, but the results have been equivocal. This trial evaluates the potential of FA to reduce enteric CH4 emissions from 18-month-old wethers fed lucerne. On two occasions, methane emissions were measured on 20 wethers fed a diet of dried ground lucerne with FA added to the diet at 0, 4, 6, 8 and 10 g FA/100 g dry matter (n = 4 wethers/treatment). Individual daily CH4 emissions were estimated using the sulfur hexafluoride (SF6) tracer gas technique together with measurements of daily dry matter intake (DMI) and total faecal output. Rumen samples were collected twice during the treatment periods in order to evaluate the effect of FA on rumen pH. There was a significant negative regression between FA% in the diet and CH4 emissions/day. However, the addition of FA did not affect CH4 emissions/kg DMI because high levels of FA supplementation reduced DMI. Rumen pH increased linearly with increasing level of FA supplementation. In conclusion, the effect of FA on CH4 emissions in this trial was associated with the resulting reduction in DMI and there were no decreases in CH4 emissions/kg DMI.
Reliability of the sulfur hexafluoride tracer technique for methane emission measurement from individual animals: an overview
Authors: Pinares-Patiño C. S. , Clark H.
Published: January 2008

Measurements of enteric methane (CH4) emissions from individual animals have traditionally been made with indirect calorimetry techniques, which are both accurate and reliable. However, the expense and need for animal training and the extent to which calorimetric results can be extrapolated to free-ranging animals have been questioned and stimulated the development of the sulfur hexafluoride (SF6) tracer technique. The tracer technique is now widely used in New Zealand and many other countries for CH4 emission measurements on grazing and pen-fed cattle, sheep, deer and alpacas. Few studies with cattle and sheep have examined the validity of the SF6 tracer technique. Most of these studies have concluded that estimations of CH4 emission by this technique do not differ from those of calorimetric techniques, though some exceptions have been reported. There is general agreement that the tracer technique is associated with large between-animal variability in the CH4 emission estimates from animals on the same diet, but it remains unknown whether this is due to the environment, housing conditions or the technique itself. High within-animal variability has also been reported from tracer CH4 measurements. There is growing evidence that CH4 emission estimates by the tracer technique are positively influenced by the permeation rate (PR) of the SF6 gas from permeation tubes and it has been suggested that fate of the tracer in the rumen rather than unrepresentative breath sample collection is the likely reason for the latter. It is concluded that although some issues related to the tracer technique need to be clarified, using a narrow range in PR and balancing of PR between treatments should be practised in order to overcome the relationship between PR and CH4 emission estimates.
Greenhouse gas emissions from New Zealand agriculture: issues, perspectives and industry response
Authors: Leslie M. , Aspin M. , Clark H.
Published: January 2008

The prosperity of New Zealand (NZ) rests to a large extent on agriculture. Although our total greenhouse gas (GHG) emissions are unusually small for a developed nation, agricultural emissions make up almost half of the total emissions from NZ. Emissions from NZ agriculture have been rising at close to 1% a year since 1990 and by 2010, the midpoint of the first commitment period of the Kyoto Protocol, they are projected to be 7.2 Mt per year higher than the 1990 baseline. This excess has a potential cost of over NZ$0.5 billion. Despite the continued rise in absolute emissions, emissions intensity, the amount of GHG produced per unit of food produced, has been dropping and the emissions intensity of NZ agriculture goods compares favourably with that of other developed nations. The NZ agricultural sector has actively engaged in the search for cost-effective mitigation solutions and, in partnership with the government, has funded research through the Pastoral Greenhouse Gas Research Consortium (PGGRC). The PGGRC has been in existence since 2002 and has invested NZ$16 million in research into reducing methane and nitrous oxide emissions from pastoral agriculture. The structure of this research funding body, its objectives, achievements and future challenges are briefly outlined.
Li-decorated metal–organic framework 5: A route to achieving a suitable hydrogen storage medium
Authors: Blomqvist A. , Araújo C. Moysés , Srepusharawoot P. , Ahuja R.
Published: January 2008

A significant improvement in molecular hydrogen uptake properties is revealed by our
ab initio
calculations for Li-decorated metal–organic framework 5. We have found that two Li atoms are strongly adsorbed on the surfaces of the six-carbon rings, one on each side, carrying a charge of +0.9e per Li atom. Each Li can cluster three H
2
molecules around itself with a binding energy of 12 kJ (mol H
2
)
−1
. Furthermore, we show from
ab initio
molecular dynamics simulations with a hydrogen loading of 18 H
2
per formula unit that a hydrogen uptake of 2.9 wt % at 200 K and 2.0 wt % at 300 K is achievable. To our knowledge, this is the highest hydrogen storage capacity reported for metal–organic framework 5 under such thermodynamic conditions.
Role of Epac1, an Exchange Factor for Rap GTPases, in Endothelial Microtubule Dynamics and Barrier Function
Authors: Sehrawat Seema , Cullere Xavier , Patel Sunita , Italiano Joseph , Mayadas Tanya N.
Published: January 2008

Rap1 GTPase activation by its cAMP responsive nucleotide exchange factor Epac present in endothelial cells increases endothelial cell barrier function with an associated increase in cortical actin. Here, Epac1 was shown to be responsible for these actin changes and to colocalize with microtubules in human umbilical vein endothelial cells. Importantly, Epac activation with a cAMP analogue, 8-pCPT-2′O-Me-cAMP resulted in a net increase in the length of microtubules. This did not require cell–cell interactions or Rap GTPase activation, and it was attributed to microtubule growth as assessed by time-lapse microscopy of human umbilical vein endothelial cell expressing fluorophore-linked microtubule plus-end marker end-binding protein 3. An intact microtubule network was required for Epac-mediated changes in cortical actin and barrier enhancement, but it was not required for Rap activation. Finally, Epac activation reversed microtubule-dependent increases in vascular permeability induced by tumor necrosis factor-α and transforming growth factor-β. Thus, Epac can directly promote microtubule growth in endothelial cells. This, together with Rap activation leads to an increase in cortical actin, which has functional significance for vascular permeability.
Infrared-Guided Laser Stimulation of Neurons in Brain Slices: Figure 1.
Authors: Dodt Hans-Ulrich , Eder Matthias , Schierloh Anja , Zieglgänsberger Walter
Published: January 2008

INTRODUCTION

This protocol describes an approach for easy and precise stimulation of single neurons in brain slices using caged neurotransmitters. The technique can be applied to neurobiological problems for which precise and rapid stimulation of neurons in brain slices is required. When a caged neurotransmitter is added to the superfusion medium, neurons in brain slices can be excited by shining light on them. This very localized application allows dendrites to be scanned for the distribution of neurotransmitter receptors. Furthermore, by the stimulation of neighboring neurons, the connectivity of neuronal networks can be investigated. As laser stimulation can be performed quickly, this technique can also be used to search for synaptic connections between distant neurons with a low probability of connectivity.
Intracellular Trafficking Studies Using Gold-Encapsulated Gelatin Nanoparticles: Figure 1.
Authors: Kommareddy Sushma , Amiji Mansoor M.
Published: January 2008

INTRODUCTION

Trafficking of nanoparticles in cells is best carried out by encapsulation of electron-dense material (e.g., gold) in the nanoparticles and by visualizing them in the cell by transmission electron microscopy (TEM). This protocol describes the preparation of gold particles, their encapsulation in protein nanoparticles, culture conditions, and sample preparation for TEM.
Cell Transfection and Analysis Using DNA-Loaded Gelatin Nanoparticles
Authors: Kommareddy Sushma , Amiji Mansoor M.
Published: January 2008

INTRODUCTION

This protocol describes cell-culture techniques for transfection using DNA-loaded gelatin nanoparticles. Also included are methods for qualitative analysis of transfection with fluorescence microscopy and quantitative analysis using a fluorescence-activated cell sorter (FACS).
Long-Term, High-Resolution Imaging in the Neocortex In Vivo
Authors: Chen Brian E. , Trachtenberg Joshua T. , Holtmaat Anthony J.G.D. , Svoboda Karel
Published: January 2008

INTRODUCTION

In the neocortex, elucidating the mechanisms of structural plasticity is essential to an understanding of the emergent network properties and fundamental cognitive phenomena, such as memory formation. Time-lapse imaging microscopy has revealed a remarkable array of dynamic activities in dendritic structures in developing cortical tissue in vitro, the developing cortex in vivo, and even the adult neocortex. Chronic high-resolution in vivo imaging of the structure of neurons in the cortex became possible with the invention of two-photon laser scanning microscopy (2PLSM). This technique has key advantages over conventional, single-photon excitation techniques, such as confocal microscopy. Two-photon excitation is the near-simultaneous (within femtoseconds) absorption of two photons coinciding on a fluorophore. The absorption rate depends quadratically on the illumination intensity and is therefore confined to a small volume around the focal point. Scattered excitation light is too weak to generate fluorescence. Thus, the signal is generated exclusively in a tiny focal volume, and all emitted fluorescence photons constitute useful signals. A related advantage is that the longer wavelengths used to generate two-photon excitation penetrate scattering tissue more efficiently than the shorter wavelengths used to generate single-photon excitation of the same fluorophores. The upper layers (1-4) of neocortex are ideal for high-resolution 2PLSM imaging. This protocol describes experimental procedures for in vivo imaging in the neocortex.
GenomePlex Whole-Genome Amplification
Authors: Arneson Nona , Hughes Simon , Houlston Richard , Done Susan
Published: January 2008

INTRODUCTION

PCR-based whole-genome amplification (WGA) has the goal of generating microgram quantities of genome-representative DNA from picogram or nanogram amounts of starting material. This amplification should introduce little, or ideally no, representational bias. In contrast to other techniques for WGA, PCR-based methods are generally less affected by DNA quality and are more applicable to DNA extracted from various sources (fixed and fresh tissues). GenomePlex WGA, described in this protocol, is a proprietary amplification technology based on nonenzymatic random fragmentation of genomic DNA. The protocol involves conversion of the genome into an in vitro molecular library of DNA fragments, followed by incubation at various temperatures to add adaptor sequences with specific PCR priming sites to both ends of every fragment. The fragment library can then be amplified several 1000-fold to generate milligram quantities of DNA starting with as little as 10-100 ng.
Transfecting Avian Motor Neurons and Their Axons Using In Ovo Electroporation
Authors: Linn Stephanie A. , Krull Catherine E.
Published: January 2008

INTRODUCTION

In ovo electroporation of half of the avian neural tube is a simple procedure in which one places the electrodes parallel to the neural tube, flanking the intended axial region of transfection. It is possible to modify this technique to target the ventral quadrant of the neural tube that contains motor neurons in the lateral motor column (LMC) and their axons by positioning the electrodes in an offset dorsal/ventral configuration, instead of the standard parallel position. If the electroporation is performed in the neural tube of stage 15 chick embryos, the medial portion of the LMC is targeted primarily; however, if neural tubes of stage 17 embryos are electroporated, the entire LMC will be transfected. This technique can be used to examine the behavior of motor axons as they project into the developing limb when genes are misexpressed, overexpressed, or knocked down via RNAi (using short hairpin RNA [shRNA]). The un-electroporated half of the neural tube serves as an internal control, or an enhanced green fluorescent protein (EGFP) reporter construct (pCAX) serves as a control for the electroporation and for EGFP expression. By electroporating a DNA construct that contains EGFP, or co-electroporating the DNA of interest with a GFP reporter construct, it is possible to verify the success of the electroporation in ovo.
Speices diversity and the systematics of some New World leaf litter Thysanoptera (Phlaeothripinae; Glyptothripini)
Authors: MOUND LAURENCE A.
Published: January 2008

Abstract More than fifty species of closely related glyptothripine Thysanoptera

have been described from leaf litter at one site in southern Brazil. The ecological and evolutionary significance of this species swarm are discussed, and the relationships of the New World glyptothripine genera are reassessed. A key is produced to the world genera of the Glyptothripini, and a check list is provided to the fifteen genera and 119 species from the New World. Nomenclatural changes include thirty‐five new combinations, five new generic synonyms and one new specific synonym.
Ectoparasitic adaptations in Forcipomyia from butterflies with two new African species (Ceratopogonidae)
Authors: LANE RICHARD P.
Published: January 2008

Abstract. Two new ectoparasities of butterflies from Africa are described: Forcipomyia (Trichohelea) monoplectron sp.n. and F.collinsi sp.n. A key for the identification of the African species ofthe subgenus Trichohelea is given. The extraodinary distribution of F.collinsi in Africa and South America is tentatively correlated with the distribution of migratory Rhopalocera. An hypothesis is presented for the functional significance of the tarsal claw modifications in this group of parasites.