bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of dicationic ionic liquids as a novel liquid platform for dielectrophoretic cell manipulation
Authors: Taruvai Kalyana Kumar Rajeshwari , De Mello Gindri Izabelle , Kinnamon David , Rodrigues Danieli C. , Frizzo Clarissa P. , Prasad Shalini
Published: February 2016

Separation, characterization and analysis of target cells demonstrate critical cues for diagnosis and monitoring of chronic diseases.
Correction: Dehydrocoupling of phosphine–boranes using the [RhCp*Me(PMe3)(CH2Cl2)][BArF4] precatalyst: stoichiometric and catalytic studies
Authors: Hooper Thomas N. , Weller Andrew S. , Beattie Nicholas A. , Macgregor Stuart A.
Published: February 2016

Correction for ‘Dehydrocoupling of phosphine–boranes using the [RhCp*Me(PMe3)(CH2Cl2)][BArF4] precatalyst: stoichiometric and catalytic studies’ by Thomas N. Hooper et al., Chem. Sci., 2016, DOI: 10.1039/c5sc04150c.
Recent structural and mechanistic insights into protein O-GalNAc glycosylation
Authors: Hurtado-Guerrero Ramon
Published: February 2016

Protein O-GalNAcylation is an abundant post-translational modification and predicted to occur in over 80% of the proteins passing through the Golgi apparatus. This modification is driven by 20 polypeptide GaINAc (N-acetylgalactosamine)-transferases (GalNAc-Ts), which are unique in that they possess both catalytic and lectin domains. The peptide substrate specificities of GalNAc-Ts are still poorly defined and our understanding of the sequence and structural features that direct O-glycosylation of proteins is limited. Part of this may be attributed to the complex regulation by coordinated action of multiple GalNAc-T isoforms, and part of this may also be attributed to the two functional domains of GalNAc-Ts that both seems to be involved in directing the substrate specificities. Recent studies have resulted in 3D structures of GalNAc-Ts and determination of the reaction mechanism of this family of enzymes. Key advances include the trapping of binary/ternary complexes in combination with computational simulations and AFM/small-SAXS experiments, which have allowed for the dissection of the reaction coordinates and the mechanism by which the lectin domains modulate the glycosylation. These studies not only broaden our knowledge of the modes-of-action of this family of enzymes but also open up potential avenues for the rational design of effective and selective inhibitors of O-glycosylation.
O-GlcNAc transferase inhibitors: current tools and future challenges
Authors: Trapannone Riccardo , Rafie Karim , van Aalten Daan M.F.
Published: February 2016

The O-linked N-acetylglucosamine (O-GlcNAc) post-translational modification (O-GlcNAcylation) is the dynamic and reversible attachment of N-acetylglucosamine to serine and threonine residues of nucleocytoplasmic target proteins. It is abundant in metazoa, involving hundreds of proteins linked to a plethora of biological functions with implications in human diseases. The process is catalysed by two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) that add and remove sugar moieties respectively. OGT knockout is embryonic lethal in a range of animal models, hampering the study of the biological role of O-GlcNAc and the dissection of catalytic compared with non-catalytic roles of OGT. Therefore, selective and potent chemical tools are necessary to inhibit OGT activity in the context of biological systems. The present review focuses on the available OGT inhibitors and summarizes advantages, limitations and future challenges.
Glycosyltransferase engineering for carbohydrate synthesis
Authors: McArthur John B. , Chen Xi
Published: February 2016

Glycosyltransferases (GTs) are powerful tools for the synthesis of complex and biologically-important carbohydrates. Wild-type GTs may not have all the properties and functions that are desired for large-scale production of carbohydrates that exist in nature and those with non-natural modifications. With the increasing availability of crystal structures of GTs, especially those in the presence of donor and acceptor analogues, crystal structure-guided rational design has been quite successful in obtaining mutants with desired functionalities. With current limited understanding of the structure–activity relationship of GTs, directed evolution continues to be a useful approach for generating additional mutants with functionality that can be screened for in a high-throughput format. Mutating the amino acid residues constituting or close to the substrate-binding sites of GTs by structure-guided directed evolution (SGDE) further explores the biotechnological potential of GTs that can only be realized through enzyme engineering. This mini-review discusses the progress made towards GT engineering and the lessons learned for future engineering efforts and assay development.
Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases
Authors: Flanagan Lindsey A. , Parkin Alison
Published: February 2016

Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.
A tale of two inositol trisphosphates
Authors: Irvine Robin
Published: February 2016

Between spring 1982 and autumn 1984 the physiological role of Ins(1,4,5)P3 as a calcium-mobilizing second messenger was first suggested and then experimentally established. At the same time the unexpected complexity of inositide metabolism began to be exposed by the discovery of Ins(1,3,4)P3. This article recalls my entanglement with these two inositol phosphates.
Does PtdIns(4,5)P2 concentrate so it can multi-task?
Authors: Hammond Gerald R.V.
Published: February 2016

Ptdns(4,5)P2 is a minor structural lipid of the plasma membrane (PM), but a master regulator of PM function. Serving either as a substrate for the generation of second messengers, or more commonly as a ligand triggering protein recruitment or activation, it regulates most aspects of PM function. Understanding how this relatively simple biological macromolecule can regulate such a vast array of different functions in parallel, is the key to understanding the biology of the PM as a whole, in both health and disease. In this review, potential mechanisms are discussed that might explain how a lipid can separately regulate so many protein complexes. The focus is on the spatial distribution of the lipid molecules, their metabolism and their interactions. Open questions that still need to be resolved are highlighted, as are potential experimental approaches that might shed light on the mechanisms at play. Moreover, the broader question is raised as to whether PtdIns(4,5)P2 should be thought of as a bona fide signalling molecule or more of a simple lipid cofactor or perhaps both, depending on the context of the particular function in question.
Caveats in studies of the physiological role of polyphosphates in coagulation
Authors: Lindahl Tomas L. , Ramström Sofia , Boknäs Niklas , Faxälv Lars
Published: February 2016

Platelet-derived polyphosphates (polyP), stored in dense granule and released upon platelet activation, have been claimed to enhance thrombin activation of coagulation factor XI (FXI) and to activate FXII directly. The latter claim is controversial and principal results leading to these conclusions are probably influenced by methodological problems. It is important to consider that low-grade contact activation is initiated by all surfaces and is greatly amplified by the presence of phospholipids simulating the procoagulant membranes of activated platelets. Thus, proper use of inhibitors of the contact pathway and a careful choice of materials for plates and tubes is important to avoid artefacts. The use of phosphatases used to degrade polyP has an important drawback as it also degrades the secondary activators ADP and ATP, which are released from activated platelets. In addition, the use of positively charged inhibitors, such as polymyxin B, to inhibit polyP in platelet-rich plasma and blood is problematic, as polymyxin B also slows coagulation in the absence of polyP. In conclusion we hope awareness of the above caveats may improve research on the physiological roles of polyP in coagulation.
The PTEN protein: cellular localization and post-translational regulation
Authors: Leslie Nick R. , Kriplani Nisha , Hermida Miguel A. , Alvarez-Garcia Virginia , Wise Helen M.
Published: February 2016

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) phosphatase dephosphorylates PIP3, the lipid product of the class I PI 3-kinases, and suppresses the growth and proliferation of many cell types. It has been heavily studied, in large part due to its status as a tumour suppressor, the loss of function of which is observed through diverse mechanisms in many tumour types. Here we present a concise review of our understanding of the PTEN protein and highlight recent advances, particularly in our understanding of its localization and regulation by ubiquitination and SUMOylation.
Sialidases from gut bacteria: a mini-review
Authors: Juge Nathalie , Tailford Louise , Owen C David
Published: February 2016

Sialidases are a large group of enzymes, the majority of which catalyses the cleavage of terminal sialic acids from complex carbohydrates on glycoproteins or glycolipids. In the gastrointestinal (GI) tract, sialic acid residues are mostly found in terminal location of mucins via α2-3/6 glycosidic linkages. Many enteric commensal and pathogenic bacteria can utilize sialic acids as a nutrient source, but not all express the sialidases that are required to release free sialic acid. Sialidases encoded by gut bacteria vary in terms of their substrate specificity and their enzymatic reaction. Most are hydrolytic sialidases, which release free sialic acid from sialylated substrates. However, there are also examples with transglycosylation activities. Recently, a third class of sialidases, intramolecular trans-sialidase (IT-sialidase), has been discovered in gut microbiota, releasing (2,7-anhydro-Neu5Ac) 2,7-anydro-N-acetylneuraminic acid instead of sialic acid. Reaction specificity varies, with hydrolytic sialidases demonstrating broad activity against α2,3-, α2,6- and α2,8-linked substrates, whereas IT-sialidases tend to be specific for α2,3-linked substrates. In this mini-review, we summarize the current knowledge on the structural and biochemical properties of sialidases involved in the interaction between gut bacteria and epithelial surfaces.
Continuous‐time digital filtering analogue‐to‐digital converter
Authors: Ratiu A. , Morche D. , Allard B. , Lin‐Shi X. , Verdier J.
Published: February 2016

Despite their alias‐free operation, continuous time ADCs can have their power consumption overwhelmed when presented out‐of‐band, high frequency, high amplitude signals. A new continuous time ADC architecture which, thanks to its embedded low‐pass filter transfer function is proposed, enables a power efficient quantisation in the presence of such signals. Moreover, the half‐digital nature of this approach simplifies the implementation of the proposed system compared to a standard filter‐first solution.
Density aware anomaly detection in crowded scenes
Authors: Gunduz Ayse Elvan , Ongun Cihan , Temizel Tugba Taskaya , Temizel Alptekin
Published: February 2016

Coherent nature of crowd movement allows representing the crowd motion using sparse features. However, surveillance videos recorded at different periods of time are likely to have different crowd densities and motion characteristics. These varying scene properties necessitate use of different models for an effective representation of behaviour at different periods. In this study, a density aware approach is proposed to detect motion‐based anomalies for scenes having varying crowd densities. In the training, the sparse features are modelled using separate hidden Markov models, each of which becomes an expert for specific scene characteristics. These models are then used for anomaly detection. The proposed method automatically adapts to the changing scene dynamics by switching to the most representative model at each frame. The authors demonstrate the effectiveness and real‐time performance of the proposed method on real‐life datasets as well as on simulated crowd videos that they generated and made publicly available to download.
Perspective: Computer simulations of long time dynamics
Authors: Elber Ron
Published: February 2016

Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
Phase field simulation of a droplet impacting a solid surface
Authors: Zhang Qian , Qian Tie-Zheng , Wang Xiao-Ping
Published: February 2016

We simulate a droplet impacting on a solid surface using a phase field model consisting of the Cahn-Hilliard and Navier Stokes equations with the generalized Navier boundary condition. An efficient gradient stable scheme is used to solve the system in axisymmetric coordinates. Our objective is to understand numerically the mechanisms leading to different impacting phenomena such as adherence, bouncing, partial bouncing, and splashing. In particular, we study how various processes are affected by the relevant dimensionless parameters: the Reynolds number, Weber number, density ratio, viscosity ratio, and the wettability of the solid surface. We also compare our numerical results with the experimental results and observe almost quantitative agreement.
Evaporation-driven clustering of microscale pillars and lamellae
Authors: Kim Tae-Hong , Kim Jungchul , Kim Ho-Young
Published: February 2016

As a liquid film covering an array of micro- or nanoscale pillars or lamellae evaporates, its meniscus pulls the elastic patterns together because of capillary effects, leading to clustering of the slender microstructures. While this elastocapillary coalescence may imply various useful applications, it is detrimental to a semiconductor manufacturing process called the spin drying, where a liquid film rinses patterned wafers until drying. To understand the transient mechanism underlying such self-organization during and after liquid evaporation, we visualize the clustering dynamics of polymer micropatterns. Our visualization experiments reveal that the patterns clumped during liquid evaporation can be re-separated when completely dried in some cases. This restoration behavior is explained by considering adhesion energy of the patterns as well as capillary forces, which leads to a regime map to predict whether permanent stiction would occur. This work does not only extend our understanding of micropattern stiction, but also suggests a novel path to control and prevent pattern clustering.
Rectified motion in an asymmetrically structured channel due to induced-charge electrokinetic and thermo-kinetic phenomena
Authors: Sugioka Hideyuki
Published: February 2016

It would be advantageous to move fluid by the gradient of random thermal noises that are omnipresent in the natural world. To achieve this motion, we propose a rectifier that uses a thermal noise along with induced-charge electroosmosis and electrophoresis (ICEO and ICEP) around a metal post cylinder in an asymmetrically structured channel and numerically examine its rectification performance. By the boundary element method combined with the thin double layer approximation, we find that rectified motion occurs in the asymmetrically structured channel due to ICEO and ICEP. Further, by thermodynamical and equivalent circuit methods, we discuss a thermal voltage that drives a rectifier consisting of a fluidic channel of an electrolyte and an impedance as a noise source. Our calculations show that fluid can be moved in the asymmetrically structured channel by the fluctuation of electric fields due to a thermal noise only when there is a temperature difference. In addition, our simple noise argument provides a different perspective for the thermo-kinetic phenomena (around a metal post) which was predicted based on the electrolyte Seebeck effect in our previous paper [H. Sugioka, “Nonlinear thermokinetic phenomena due to the Seebeck effect,” Langmuir 30, 8621 (2014)].
On Wigner transforms in infinite dimensions
Authors: Beltiţă Ingrid , Beltiţă Daniel , Măntoiu Marius
Published: February 2016

We investigate the Schrödinger representations of certain infinite-dimensional Heisenberg groups, using their corresponding Wigner transforms.
Single shot spin readout using a cryogenic high-electron-mobility transistor amplifier at sub-Kelvin temperatures
Authors: Tracy L. A. , Luhman D. R. , Carr S. M. , Bishop N. C. , Ten Eyck G. A. , Pluym T. , Wendt J. R. , Lilly M. P. , Carroll M. S.
Published: February 2016

We use a cryogenic high-electron-mobility transistor circuit to amplify the current from a single electron transistor, allowing for demonstration of single shot readout of an electron spin on a single P donor in Si with 100 kHz bandwidth and a signal to noise ratio of ∼9. In order to reduce the impact of cable capacitance, the amplifier is located adjacent to the Si sample, at the mixing chamber stage of a dilution refrigerator. For a current gain of ∼2.7×103, the power dissipation of the amplifier is 13 μW, the bandwidth is ∼1.3 MHz, and for frequencies above 300 kHz the current noise referred to input is ≤70 fA/Hz. With this amplification scheme, we are able to observe coherent oscillations of a P donor electron spin in isotopically enriched 28Si with 96% visibility.
Transport equation for plasmas in a stationary-homogeneous turbulence
Authors: Wang Shaojie
Published: February 2016

For a plasma in a stationary homogeneous turbulence, the Fokker-Planck equation is derived from the nonlinear Vlasov equation by introducing the entropy principle. The ensemble average in evaluating the kinetic diffusion tensor, whose symmetry has been proved, can be computed in a straightforward way when the fluctuating particle trajectories are provided. As an application, it has been shown that a mean parallel electric filed can drive a particle flux through the Stokes-Einstein relation, independent of the details of the fluctuations.
Sheep greenhouse gas emission intensities under different management practices, climate zones and enterprise types
Authors: Cottle D. J. , Harrison M. T. , Ghahramani A.
Published: February 2016

Greenhouse gas emissions (GHG) from broadacre sheep farms constitute ~16% of Australia’s total livestock emissions. To study the diversity of Australian sheep farming enterprises a combination of modelling packages was used to calculate GHG emissions from three sheep enterprises (Merino ewe production for wool and meat, Merino-cross ewes with an emphasis on lamb production, and Merino wethers for fine wool production) at 28 sites across eight climate zones in southern Australia. GHG emissions per ha, per dry sheep equivalents and emissions intensity (EI) per tonne of clean wool or liveweight sold under different pasture management or animal breeding options (that had been previously determined in interviews with farmers) were assessed relative to baseline farms in each zone (‘Nil’ option). Increasing soil phosphorus fertility or sowing 40% of the farm area to lucerne resulted in the smallest and largest changes in GHG/dry sheep equivalents, respectively (–66%, 113%), though both of these options had little influence on EI for either clean wool or liveweight sold. Breeding ewes with greater body size or genotypes with higher fleece weight resulted in 11% and 9% reductions, respectively, in EI. Enterprises specialising in lamb production (crossbred ewes) had 89% lower EI than enterprises specialising in fine wool production (Merino wethers). Thus, sheep producers aiming for lower EI could focus more on liveweight turnoff than wool production. Emissions intensities were typically highest in cool temperate regions with high rainfall and lowest in semiarid and arid regions with low aboveground net primary productivity. Overall, animal breeding options reduced EI more than feedbase interventions.
Predicting enteric methane emission in sheep using linear and non-linear statistical models from dietary variables
Authors: Patra A. K. , Lalhriatpuii M. , Debnath B. C.
Published: February 2016

The objective of the present study was to develop linear and non-linear statistical models for prediction of enteric methane emission (EME) in sheep. A database from 80 publications, which included a total of 449 mean observations of EME measured on more than 1500 sheep, was constructed to develop prediction and evaluation of models of EME. Dietary nutrient composition (g/kg), nutrient or energy intake (kg/day or MJ/day) and digestibility (g/kg) of organic matter were used as predictors of EME (MJ/day). The dietary concentrations of neutral detergent fibre and crude protein, and feed intake, were 435 g/kg, 152 g/kg and 0.92 kg/day, respectively. The EME by sheep expressed as MJ/day and % of gross energy intake was 1.02 and 6.54, respectively. The simple linear equation that predicted EME with high precision and accuracy was EME = 0.208(±0.040) + 0.049(±0.0039) × gross energy intake (MJ/day), adjusted R2 = 0.86 with root mean-square prediction error of 22.7%, of which 93% was from random error and regression bias of 3.20%. Additions of dietary concentration of fibre and feeding level, and organic matter digestibility to the simple linear model improved the models. Among the non-linear equations developed, monomolecular model, i.e. EME = 5.699 (±1.94) – [5.699 (±1.94) – 0.133 (±0.047)] × exp[–0.021(±0.0071) × metabolisable energy intake (MJ/day)]; adjusted R2 = 0.90 and mean-square prediction error = 20.1%, with 96.3% random error, performed better than simple linear and other non-linear models. The equations developed in the present study will be useful for national methane inventory preparation, and for a better understanding of dietary factors influencing EME in sheep.
Repeatability of enteric methane determinations from cattle using either the SF6 tracer technique or the GreenFeed system
Authors: Arbre M. , Rochette Y. , Guyader J. , Lascoux C. , Gómez L. M. , Eugène M. , Morgavi D. P. , Renand G. , Doreau M. , Martin C.
Published: February 2016

The SF6 tracer technique (SF6) and GreenFeed system (GF) are two methods for measuring enteric methane (CH4) emissions from cattle. Both methods estimate individual daily CH4 emissions from expired gas samples collected either continuously over 24 h in a canister (SF6) or several times a day during short-term periods (3–8 min) when cattle visit an automated head chamber (GF). The objective of this work was to study repeatability (R) of each method according to duration of measurement period as an indicator of their precision. The R of CH4 measurements was evaluated in two different trials using cows. For Experiment 1, the SF6 technique was used for 20 days in six non-lactating dairy cows fed a hay-based diet; for Experiment 2, the GF system was used for 91 days in seven lactating dairy cows fed a maize silage-based diet. The CH4 data were grouped by periods of 1–10 days (SF6) and 1–45 days (GF). The CH4 emissions averaged 23.6 ± 3.9 g/kg dry matter intake (DMI) for the SF6 and 17.4 ± 3.3 g/kg DMI for the GF on the measurement period. To achieve an R value of 0.70 for CH4 emissions (g/kg DMI), 3-day periods were necessary for SF6 and 17-day periods for GF. The R did not increase after 4-day periods for SF6 (R = 0.73), but increased for GF until 45-day periods (R = 0.90). In our experimental conditions and R = 0.70, the total number of cows necessary to detect a significant difference in CH4 emissions (g/kg DMI) between two treatments (e.g. diet) was similar for SF6 and GF.
Using airborne technology to quantify and apportion emissions of CH4 and NH3 from feedlots
Authors: Hacker Jorg M. , Chen Deli , Bai Mei , Ewenz Caecilia , Junkermann Wolfgang , Lieff Wolfgang , McManus Barry , Neininger Bruno , Sun Jianlei , Coates Trevor , Denmead Tom , Flesch Thomas , McGinn Sean , Hill Julian
Published: February 2016

A novel airborne approach using the latest technology in concentration measurements of methane (CH4) and ammonia (NH3), with quantum cascade laser gas analysers (QCLAs) and high-resolution wind, turbulence and other atmospheric parameters integrated into a low- and slow-flying modern airborne platform, was tested at a 17 000 head feedlot near Charlton, Victoria, Australia, in early 2015. Aircraft flights on 7 days aimed to define the lateral and vertical dimensions of the gas plume above and downwind of the feedlot and the gas concentrations within the plume, allowing emission rates of the target gases to be calculated. The airborne methodology, in the first instance, allowed the emissions to be qualitatively apportioned to individual rows of cattle pens, effluent ponds and manure piles. During each flight, independent measurements of emissions were conducted by ground-based inverse-dispersion and eddy covariance techniques, simultaneously. The aircraft measurements showed good agreement with earlier studies using more traditional approaches and the concurrent ground-based measurements. It is envisaged to use the aircraft technology for determining emissions from large-scale open grazing farms with low cattle densities. Our results suggested that this technique is able to quantify emissions from various sources within a feedlot (pens, manure piles and ponds), as well as the whole feedlot. Furthermore, the airborne technique enables tracing emissions for considerable distances downwind. In the current case, it was possible to detect elevated CH4 to at least 25 km and NH3 at least 7 km downwind of the feedlot.
Effect of short-term infusion of hydrogen on enteric gas production and rumen environment in dairy cows
Authors: Olijhoek D. W. , Hellwing A. L. F. , Weisbjerg M. R. , Dijkstra J. , Højberg O. , Lund P.
Published: February 2016

Methane (CH4) production by rumen methanogens lowers hydrogen (H2) pressure and, in theory, prevents inhibition of fermentation processes by H2 accumulation. The present study aimed at examining effects of short-term H2 infusion on CH4 production and the volatile fatty acid (VFA) profile. Four lactating Holstein dairy cows fitted with rumen cannula were each infused once with pure H2 into the rumen at a rate of 48.0 L/h during 5.75 h in between the morning and afternoon feeding. Gas exchange and feed intake were measured continuously by open-circuit respiration chambers during 5 days. Rumen liquid was sampled twice a day in connection with milking and feeding (0630 hours and 1700 hours) and analysed for VFA. Gas exchange and dry matter intake (DMI) were analysed for 5-h steady-state H2 concentrations (TI5) measured in respiration chambers and for 24-h time intervals (TI24) on the day before, during and after infusion. Hydrogen infusion did not affect the total VFA concentration and VFA molar proportions for either time interval. Methane production was higher for TI5 during infusion (130 L/5 h) than it was the day before infusion (120 L/5 h), but not the day after infusion (122 L/5 h). Methane production for TI24 and DMI for TI5 and TI24 were unaffected. Oxygen consumption and CH4 : CO2 were highest during infusion for TI5, but not for TI24. After correcting for H2 naturally produced, on average, 46.7 L H2/h was measured during TI5, indicating that 2.7% of the infused H2 was retained in the rumen. In conclusion, H2 infusion did not affect the VFA profile, but slightly increased CH4 production and CH4 : CO2.
Manure distribution as a predictor of N2O emissions from soil
Authors: Petersen S. O. , Baral K. R. , Arthur E.
Published: February 2016

Predicting nitrous oxide (N2O) emissions from manure-amended soil remains a challenge. One reason may be that spatial heterogeneity in distribution of manure is not accounted for in models of N2O emission, but experimental results suggest that both manure and soil properties affect the distribution of manure constituents after field application in a systematic way. Key to predicting the fate of labile carbon (C) and nitrogen (N) in manure is to acknowledge that the liquid phase, and a corresponding fraction of labile C and N, is partly absorbed by the bulk soil in response to the water potential gradient, and partly retained by particulate manure organic matter. Therefore, boundary conditions for subsequent transformations of C and N may be better described as two separate compartments. In this study, N2O emissions were determined in a 42-day experiment that included two soils (7.5% and 17% clay) adjusted to three soil water potentials (–3, –5 and –10 kPa) and amended with surface-applied pig slurry, cattle slurry, digestate or water only, in total 24 treatments. Net emissions of N2O corresponded to between 0.18% and 0.64% of manure N. Experimental results were analysed with a conceptual model of short-term N2O emissions from manure-amended soil, which estimates redistribution of manure constituents and predicts emissions from three sources, i.e. nitrification in bulk soil, and nitrification and denitrification in manure hotspots. Adopting a recent modification, oxygen availability in manure hotspots was related to relative soil gas diffusivity. Model efficiencies were 42% and 12% for the two soil types when using parameters determined by multiple regression of experimental results. With the process-based model Manure-DNDC as reference, the importance of accounting for distribution of manure water and labile C and N is discussed.
Carbon-neutral wool farming in south-eastern Australia
Authors: Doran-Browne Natalie A. , Ive John , Graham Phillip , Eckard Richard J.
Published: February 2016

Ruminant livestock production generates higher levels of greenhouse gas emissions (GHGE) compared with other types of farming. Therefore, it is desirable to reduce or offset those emissions where possible. Although mitigation options exist that reduce ruminant GHGE through the use of feed management, flock structure or breeding management, these options only reduce the existing emissions by up to 30% whereas planting trees and subsequent carbon sequestration in trees and soil has the potential for livestock emissions to be offset in their entirety. Trees can introduce additional co-benefits that may increase production such as reduced salinity and therefore increased pasture production, shelter for animals or reduced erosion. Trees will also use more water and compete with pastures for water and light. Therefore, careful planning is required to locate trees where the co-benefits can be maximised instead of any negative trade-offs. This study analysed the carbon balance of a wool case study farm, Talaheni, in south-eastern Australia to determine if the farm was carbon neutral. The Australian National Greenhouse Gas Inventory was used to calculate GHGE and carbon stocks, with national emissions factors used where available, and otherwise figures from the IPCC methodology being used. Sources of GHGE were from livestock, energy and fuel, and carbon stocks were present in the trees and soil. The results showed that from when the farm was purchased in 1980–2012 the farm had sequestered 11 times more carbon dioxide equivalents (CO2e) in trees and soil than was produced by livestock and energy. Between 1980 and 2012 a total of 31 100 t CO2e were sequestered with 19 300 and 11 800 t CO2e in trees and soil, respectively, whereas farm emissions totalled 2800 t CO2e. There was a sufficient increase in soil carbon stocks alone to offset all GHGE at the study site. This study demonstrated that there are substantial gains to be made in soil carbon stocks where initial soils are eroded and degraded and there is the opportunity to increase soil carbon either through planting trees or introducing perennial pastures to store more carbon under pastures. Further research would be beneficial on the carbon-neutral potential of farms in more fertile, high-rainfall areas. These areas typically have higher stocking rates than the present study and would require higher levels of carbon stocks for the farm to be carbon neutral.
Comparative analysis of greenhouse gas emissions from three beef cattle herds in a corporate farming enterprise
Authors: Taylor Chris , Eckard Richard
Published: February 2016

This study provided a gate-to-gate Life Cycle Assessment that modelled the greenhouse gas emissions (GHG) of three herds bred and grown by an integrated beef cattle enterprise across northern Australia. It involved modelling the GHG emissions of current herd management by the enterprise as a ‘baseline’ compared with ‘alternative scenarios’ of herd management. There were three herds (one herd of steers and two herds of heifers) each consisting of 5000 head of cattle. The baseline consisted of the steer herd grazing on growing then backgrounding properties and being finished at a feedlot. The two heifer herds grazed one respective backgrounding property each and were finished in a feedlot for their respective baselines. The alternative scenarios involved the steer herd bypassing the growing property and spending increased time at the backgrounding property. The heifer herds bypassed their respective backgrounding properties and they were grown and finished at a feedlot. The results show a 14% reduction of GHG emission intensities between the baseline and alternative scenario for steers and reductions of 29% and 4% between the baseline and alternative scenarios for the respective heifer herds. The variance in GHG emissions between the heifer herds can be explained by relative time spent grazing on the respective backgrounding properties and associated liveweight gain, versus time spent being grown and finished in the feedlot. In our modelling, herd GHG emission reductions occurred in the scenarios when time grazing on the growing or backgrounding properties (and associated liveweight gains) in the respective baselines exceeded 225–229 days for the heifer herds and between 206 days for the steers (depending on the relative liveweight gains on the properties). This means that if the cattle herds were to spend a longer time grazing on a property in their respective baselines than the number of days noted in our analysis, bypassing these properties would then result in net reductions in GHG emissions for the herds.
Effect of rhubarb (Rheum spp.) root on in vitro and in vivo ruminal methane production and a bacterial community analysis based on 16S rRNA sequence
Authors: Kim Kyoung Hoon , Arokiyaraj Selvaraj , Lee Jinwook , Oh Young Kyoon , Chung Ho Young , Jin Gwi-Deuk , Kim Eun Bae , Kim Eun Kyoung , Lee Yoonseok , Baik Myunggi
Published: February 2016

The objective of this study was to evaluate the anti-methanogenic effect of rhubarb (Rheum spp.) on in vitro, in vivo, and bacterial community composition using Quantitative Insights into Microbial Ecology sequencing. Rhubarb root powder was tested at different concentrations (0, 0.33, 0.67, and 1.33 g/L) in vitro, and all incubations were carried out in triplicate two runs on separate days. Concentrations of 0.67 and 1.33 g/L rhubarb significantly (P < 0.05) reduced methane production and the acetate : propionate ratio compared with those of the Control, without adverse effects on total volatile fatty acids and total gas production. In the second in vivo trial, four Hanwoo (Korean native) steers (live bodyweight, 556 ± 46 kg) with a ruminal cannula were housed individually in metabolic stalls and fed a basal diet twice daily in equal amounts at 0900 hours and 2100 hours. The before rhubarb treatment (before treatment) duration was 24 days for all steers; 14 days were used for diet adaptation and 10 days were used for gas samples collected 1, 2, and 3 h after the morning feeding on Days 3, 5, 7, and 9. We used three syringe needles passed through the ruminal cannula stopper at different time points as a simple and rapid method to sample rumen gas. Thereafter, three mesh bags containing 30 g of sliced rhubarb root each were placed at different depths in the rumen of each steer for 14 days (after treatment), and gas samples were collected on Days 4, 7, 10, 12, and 13. The results showed a significant (P < 0.05) decrease in methane concentration from the rhubarb-treated steers and provide the evidence that this method would be useful for in vivo screening of anti-methanogenic feed additives or plant material. Furthermore, 16s RNA sequencing after treatment showed increases in the numbers of Prevotella, and Lactobacillus, but decreases in Methanobrevibacter. In conclusion, rhubarb had an anti-methanogenic effect in vitro and in vivo, and the increase in the number of Prevotella shifted ruminal fermentation towards propionate production.
Effects of plants containing secondary metabolites as feed additives on rumen metabolites and methanogen diversity of buffaloes
Authors: Samal L. , Chaudhary L. C. , Agarwal N. , Kamra D. N.
Published: February 2016

Four fistulated adult Murrah buffaloes were fed on a basal diet consisting of wheat straw and concentrate mixture in a 4 × 4 Latin square design to study the effects of feeding plants containing secondary metabolites on rumen metabolites and methanogen diversity. The four groups were Control (no additive), Mix-1 (ajwain oil and lemon grass oil in a 1 : 1 ratio @ 0.05% of dry matter intake), Mix-2 (garlic and soapnut in a 2 : 1 ratio @ 2% of dry matter intake) and Mix-3 (garlic, soapnut, harad and ajwain in a 2 : 1 : 1 : 1 ratio @ 1% of dry matter intake). In each phase of 30 days’ duration, after 19 days of feeding, rumen liquor was sampled for two consecutive days at 0, 2, 4, 6 and 8 h post-feeding, whereas rumen content was sampled at 0 h feeding. The pH of the rumen liquor was recorded at every collection and then the rumen liquor of every collection was pooled day-wise and animal-wise. These pooled samples were used for estimation of rumen metabolites like ammonia, lactic acid and volatile fatty acids. Microscopic counting of protozoa was done in both 0 h and pooled samples of rumen liquor. Rumen contents collected from different locations of rumen were processed for enzyme estimation. The rumen contents were squeezed and the liquid portion was used for DNA isolation, which was further processed to determine methanogen diversity. Daily intake of feed was similar (P > 0.05) in all the four groups. The ammonia-N concentration and ciliate protozoa population were reduced significantly in the treatment groups supplemented with additives. Rumen pH, lactic acid, volatile fatty acids and enzyme activities were not affected (P > 0.05) by feeding of any of these additives. Methanogenic diversity comparison was made between the Control and Mix-1 group. The basic local alignment search tool (BLAST) analysis of the 133 (44 from the Control group and 89 from the Mix-1 group) sequences showed similarity of the sequences of rumen archaea by up to 97% to the known sequences of rumen methanogens. The sequences with minimum length of 750 bp were selected for phylogenetic analysis. Per cent identity of these sequences with that of the available nearest neighbour as calculated by MEGA 5.03 software showed identity of the clones in the range of 88–97%. The clones were similar with Methanobrevibacter smithii ATCC 35061, uncultured Methanobrevibacter sp. clone MEME95 and M. ruminantium M1. Overall, feeding of any of these feed additives to fistulated buffaloes did not affect feed intake, rumen pH, or rumen metabolites except ammonia and enzyme profile. Methanogen diversity showed the possibility of Methanobrevibacter as the major methanogen in buffalo rumen liquor.
Can adaptation to nitrate supplementation and provision of fermentable energy reduce nitrite accumulation in rumen contents in vitro?
Authors: de Raphélis-Soissan V. , Nolan J. V. , Newbold J. R. , Godwin I. R. , Hegarty R. S.
Published: February 2016

Nitrate (NO3–) supplementation is a promising methane mitigation strategy for ruminants, but can cause nitrite (NO2–) poisoning. Because some nitrite reductases are NADH-dependent, we hypothesised that replacing glucose with glycerol would increase the NADH yield and so enhance nitrite reductase activity and reduce ruminal NO2– accumulation and toxicity risk. We also hypothesised that adapting sheep to dietary NO3– would limit the accumulation of NO2– when NO3– was added to rumen fluid. Changes in NO3– and NO2– catabolism and CH4 production, resulting from supplementation with glycerol to enhance NADH supply, were studied in vitro. In Experiment 1, rumen fluid from sheep adapted to dietary NO3– (2% of DM intake) or urea (1.1% of DM intake) was incubated with NO3– or urea, respectively. Additionally, ground oaten hay was added to incubations alone (control), or with glucose or glycerol. In Experiement 2, sheep were adapted for 9 weeks to dietary NO3– or urea. Nitrate (2% NO3– of substrate DM) was added to incubated digesta from NO3–- or urea-supplemented sheep, while urea (1.1% of substrate DM) was added to digesta from urea-supplemented sheep. In both studies, triplicate incubations were terminated at nine time points up to 24 h. Methane emissions were lower in all NO3– treatments (P < 0.05). Contrary to our hypotheses, both glycerol supplementation (Experiment 1) and prior adaptation to NO3– (Experiment 2) increased NO2– accumulation. In Experiment 1, there was no difference in ruminal NO2– concentration between the unsupplemented control and added glucose treatments. Nitrous oxide accumulated in NO3– treatments only with rumen fluid from sheep adapted to dietary urea (P < 0.05). In summary, NO2– accumulation in vitro was not reduced by adaptation to NO3– or by glucose or glycerol supplementation, disproving the hypotheses regarding the role of NADH availability and of NO2– adaptation in reducing ruminal NO2– accumulation and toxicity risk.
Frost-tolerance genes Fr-A2 and Fr-B2 in Australian wheat and their effects on days to heading and grain yield in lower rainfall environments in southern Australia
Authors: Eagles H. A. , Wilson Jayne , Cane Karen , Vallance Neil , Eastwood R. F. , Kuchel Haydn , Martin P. J. , Trevaskis Ben
Published: February 2016

FROST RESISTANCE 2 (FR2) genes of wheat are C-Repeat Binding Factor (CBF) genes with two major alleles known for both Fr-A2 (‘T’ and ‘S’) and Fr-B2 (‘WT’ and ‘DEL’). VERNALIZATION 1 (VRN1) genes have a regulatory role on CBF genes, with known epistatic interactions between Vrn-A1 and Fr-A2 for tolerance to freezing temperatures during vegetative growth. VRN1 genes were also known to affect days to heading and grain yield. Therefore, FR2 genes might also affect these traits.
A wide range of cultivars was characterised for VRN1, Fr-A2 and Fr-B2 genes. A third allele of Fr-A2 was found in cvv Excalibur and Axe. The winter cultivar Norstar, which was known to have a high level of frost tolerance during vegetative growth, had the combination Vrn-A1w + Fr-A2T + Fr-B2WT, as did a spring landrace from Afghanistan that was known to have superior tolerance to frost during reproductive development. No Australian spring cultivar was found with this combination, but it could be selected from crosses between adapted cultivars. This would enable the role of VRN1 and FR2 alleles in reproductive frost tolerance to be evaluated in an adapted background. Using large, existing, plant-breeding datasets, the T allele of Fr-A2 delayed heading relative to the S allele, and the WT allele of Fr-B2 delayed heading relative to the DEL allele, but only in combination with particular alleles of the VRN1 genes. Fr-B2 affected grain yield, with the highest grain yields for spring lines produced by Fr-B2DEL in combination with the spring allele of Vrn-B1.
Awareness, attitudes and practices of first aid among school teachers in Mangalore, south India
Authors: Joseph Nitin , Narayanan Thanneermalai , bin Zakaria Saifuddin , Venugopal Nair Abhishek , Belayutham Lavina , Mihiraa Subramanian Aathiya , G Gopakumar K
Published: February 2016

INTRODUCTION: Circumstances requiring medical attention are common at schools. Teachers are often the first individuals to witness and handle situations requiring first aid and medical emergencies. AIM: To determine awareness, attitudes and practices of school teachers and the facilities available at schools with respect to administration of first aid. METHODS: Data were obtained from 146 teachers in nine schools in Mangalore, India, using a self-administered questionnaire. The schools were also inspected for first aid equipment and facilities. RESULTS: Only 69 (47%) teachers had received first aid training previously. Poor and moderate knowledge of first aid was observed among 19 (13%) and 127 (87%) teachers, respectively. Only eight teachers knew the correct procedure for cardiopulmonary resuscitation. Most teachers 96 (66%) were willing to administer first aid if provided with the required training. A total of 74 teachers reported having practised first aid in response to a situation arising at their school. Wounds (36%) and syncopal attack (23%) were among the commonly encountered situations requiring first aid management at schools. Teachers? confidence level in administering first aid was significantly associated with prior training in first aid (p=0.001). First aid kits were available in only five of the nine schools surveyed. DISCUSSION: The current competency level among teachers in Mangalore to administer first aid is inadequate. Measures need to be taken at schools to ensure initiation of first aid training followed by periodic training for teachers in first aid. KEYWORDS: First aid; health knowledge, attitudes, practice; India; schools