Effect of stage of lactation and dietary starch content on endocrine-metabolic status, blood amino acid concentrations, milk yield, and composition in Holstein dairy cows.

Milk yield and composition are modified by level and chemical characteristics of dietary energy and protein. Those factors determine nutrient availability from a given diet, and once absorbed, they interact with the endocrine system and together determine availability of metabolites to the mammary gland. Four multiparous dairy cows in early lactation and subsequently in late lactation were fed 2 diets for 28 d in a changeover design that provided, within the same stage of lactation, similar amounts of rumen fermentable feed with either high (HS) or low starch (LS). All diets had similar dietary crude protein (15.5% dry matter) and rumen-undegradable protein (∼40% of crude protein) content. Profiles of AA were calculated to be similar to that of casein. On d 28, [1-13C] Leu was infused into one jugular vein with blood samples taken at 0, 2, 4, 6, and 8 h, and cows milked at 0, 2, 4, 5, 6, 7, and 8 h from start of infusion. Isotopic enrichments of plasma Leu, keto-isocaproic acid, and milk casein were determined for calculation of Leu kinetics. Data were subjected to ANOVA using the MIXED procedure of SAS (SAS Institute Inc.), with time as repeated factor and cow as the random effect. Dry matter intake within each stage of lactation was similar between groups. Feeding LS resulted in lower blood glucose and greater ratio of bovine somatotropin to insulin. This response was associated with greater blood concentrations of nonesterified fatty acids and ß-hydroxybutyrate, which might have contributed to greater milk fat content in LS-fed cows. Except for His, average concentrations of all AA in blood were higher in late than early lactation. Diet did not alter average plasma concentrations of AA. However, for most of the essential AA (particularly branched-chain), the HS diet led to a marked decrease in concentrations after the forage meal, resulting in significant differences between dietary groups in early lactation. In early-lactating cows fed HS, a greater reduction in plasma concentrations at 8 h relative to pre-feeding values (time zero) was observed for Met, Lys, and His, resulting in decreases of 27.9%, 33.6%, and 38.5%, respectively. A higher bovine somatotropin/insulin ratio in early lactation and in cows fed LS could possibly have led to greater breakdown and, consequently, higher AA flux from peripheral tissues. In LS-fed cows, higher mobilization of body fat and protein was confirmed by the greater body weight loss in both stages of lactation. Higher irreversible loss of [1-13C] Leu in early lactation suggested lower protein retention in peripheral tissues during early compared with late lactation. Milk yield, protein output, and composition were similar between groups at both stages of lactation, whereas milk coagulation was faster (lower curd firming rate) and with higher curd firmness in response to feeding HS in late lactation. Overall, data indicated that rate of carbohydrate fermentability in the rumen can modify the availability of metabolites to the mammary gland and consequently modify milk protein coagulation.

Van Hove singularity in the magnon spectrum of the antiferromagnetic quantum honeycomb lattice.

In quantum magnets, magnetic moments fluctuate heavily and are strongly entangled with each other, a fundamental distinction from classical magnetism. Here, with inelastic neutron scattering measurements, we probe the spin correlations of the honeycomb lattice quantum magnet YbCl3. A linear spin wave theory with a single Heisenberg interaction on the honeycomb lattice, including both transverse and longitudinal channels of the neutron response, reproduces all of the key features in the spectrum. In particular, we identify a Van Hove singularity, a clearly observable sharp feature within a continuum response. The demonstration of such a Van Hove singularity in a two-magnon continuum is important as a confirmation of broadly held notions of continua in quantum magnetism and additionally because analogous features in two-spinon continua could be used to distinguish quantum spin liquids from merely disordered systems. These results establish YbCl3 as a benchmark material for quantum magnetism on the honeycomb lattice.

Effect of Surface Morphology and Magnetic Impurities on the Electronic Structure in Cobalt-Doped BaFe2As2 Superconductors.

Combined scanning tunneling microscopy, spectroscopy, and local barrier height (LBH) studies show that low-temperature-cleaved optimally doped Ba(Fe1-xCox)2As2 crystals with x = 0.06, with Tc = 22 K, have complicated morphologies. Although the cleavage surface and hence the morphologies are variable, the superconducting gap maps show the same gap widths and nanometer size inhomogeneities irrelevant to the morphology. Based on the spectroscopy and LBH maps, the bright patches and dark stripes in the morphologies are identified as Ba- and As-dominated surface terminations, respectively. Magnetic impurities, possibly due to Co or Fe atoms, are believed to create local in-gap state and, in addition, suppress the superconducting coherence peaks. This study will clarify the confusion on the cleavage surface terminations of the Fe-based superconductors and its relation with the electronic structures.

Electronic structure and electron-phonon coupling in TiH2.

Calculations using first principles methods and strong coupling theory are carried out to understand the electronic structure and superconductivity in cubic and tetragonal TiH2. A large electronic density of states at the Fermi level in the cubic phase arises from Ti-t2g states and leads to a structural instability towards tetragonal distortion at low temperatures. However, constraining the in-plane lattice constants diminishes the energy gain associated with the tetragonal distortion, allowing the cubic phase to be stable at low temperatures. Calculated phonon dispersions show decoupled acoustic and optic modes arising from Ti and H vibrations, respectively, and frequencies of optic modes to be rather high. The cubic phase has a large electron-phonon coupling parameter λ and critical temperature of several K. Contribution of the hydrogen sublattice to λ is found to be small in this material, which we understand from strong coupling theory to be due to the small H-s DOS at the Fermi level and high energy of hydrogen modes at the tetrahedral sites.

The role of isovalency in the reactions of the cyano (CN), boron monoxide (BO), silicon nitride (SiN), and ethynyl (C2H) radicals with unsaturated hydrocarbons acetylene (C2H2) and ethylene (C2H4).

The classification of chemical reactions based on shared characteristics is at the heart of the chemical sciences, and is well exemplified by Langmuir's concept of isovalency, in which 'two molecular entities with the same number of valence electrons have similar chemistries'. Within this account we further investigate the ramifications of the isovalency of four radicals with the same X(2)Σ(+) electronic structure - cyano (CN), boron monoxide (BO), silicon nitride (SiN), and ethynyl (C2H), and their reactions with simple prototype hydrocarbons acetylene (C2H2) and ethylene (C2H4). The fact that these four reactants own the same X(2)Σ(+) electronic ground state should dictate the outcome of their reactions with prototypical hydrocarbons holding a carbon-carbon triple and double bond. However, we find that other factors come into play, namely, atomic radii, bonding orbital overlaps, and preferential location of the radical site. These doublet radical reactions with simple hydrocarbons play significant roles in extreme environments such as the interstellar medium and planetary atmospheres (CN, SiN and C2H), and combustion flames (C2H, BO).

Quantum dynamics study of the competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene.

Time-resolved photoelectron spectroscopy can obtain detailed information about the dynamics of a chemical process on the femtosecond timescale. The resulting signal from such detailed experiments is often difficult to analyze and therefore theoretical calculations are important in providing support. In this paper we continue our work on the competing pathways in the photophysics and photochemistry of benzene after excitation into the "channel 3" region [R. S. Minns, D. S. N. Parker, T. J. Penfold, G. A. Worth, and H. H. Fielding, Phys. Chem. Chem. Phys. 12, 15607 (2010)] with details of the calculations shown previously, building on a vibronic coupling Hamiltonian [T. J. Penfold and G. A. Worth, J. Chem. Phys. 131, 064303 (2009)] to include the triplet manifold. New experimental data are also presented suggesting that an oscillatory signal is due to a hot band excitation. The experiments show that signals are obtained from three regions of the potential surfaces, three open channels, which are assigned with the help of simulations showing that following excitation into vibrationally excited-states of S(1) the wavepacket not only crosses through the prefulvenoid conical intersection back to the singlet ground state, but also undergoes ultrafast intersystem crossing to low lying triplet states. The model is, however, not detailed enough to capture the full details of the oscillatory signal due to the hot band.

Gas-phase synthesis of the silaisocyanoethylene molecule (C2H3NSi).

The gas-phase reaction between the silicon nitride radical (SiN) and the prototypical olefin--ethylene--is investigated experimentally and theoretically for the first time. Silicon nitride (SiN) and the cyano radical (CN) are isoelectronic; however, their chemical reactivities and structures are drastically different from each other. Through the use of the cross molecular beam technique, we were able to study the notoriously refractory silicon nitride radical in reaction with ethylene under single-collision conditions. We investigated the similarities and also the distinct differences with the cyano radical-ethylene system. We find that the silicon nitride radical bonds by the nitrogen atom to the double bond of ethylene; in comparison, the cyano radical adds via its carbon atom. The silicon nitride addition is barrierless, forming a long-lived SiNCH(2)CH(2) collision complex, which is also able to isomerize via a hydrogen shift to the SiNCHCH(3) intermediate. Both isomers can emit a hydrogen atom via tight transition states to form the silaisocyanoethylene (SiNC(2)H(3)) molecule in an overall exoergic reaction. This presents the very first experiment in which the silaisocyanoethylene molecule--a member of the silaisocyanide family--has been formed via a directed synthesis under gas-phase single-collision conditions. In comparison with the isoelectronic cyano-ethylene system, the cyanoethylene (C(2)H(3)CN) isomer is formed. Therefore, the replacement of a single carbon atom by an isovalent silicon atom, i.e. shifting from the cyano (CN) to the silicon nitride (SiN) radical, has a dramatic influence not only on the reactivity with ethylene (carbon atom versus nitrogen atom addition) but also on the final reaction products. In the reactions of ethylene with silicon nitride and the cyano radical, the silaisonitrile over the silanitrile and the nitrile over the isonitrile reaction products are favored, respectively. This reaction provides rare experimental data for investigating the chemistry of bimolecular reactions of silicon nitride diatomics in chemical vapor deposition techniques and interstellar environments.

PAH formation under single collision conditions: reaction of phenyl radical and 1,3-butadiene to form 1,4-dihydronaphthalene.

The crossed beam reactions of the phenyl radical (C(6)H(5), X(2)A(1)) with 1,3-butadiene (C(4)H(6), X(1)A(g)) and D6-1,3-butadiene (C(4)D(6), X(1)A(g)) as well as of the D5-phenyl radical (C(6)D(5), X(2)A(1)) with 2,3-D2-1,3-butadiene and 1,1,4,4-D4-1,3-butadiene were carried out under single collision conditions at collision energies of about 55 kJ mol(-1). Experimentally, the bicyclic 1,4-dihydronaphthalene molecule was identified as a major product of this reaction (58 ± 15%) with the 1-phenyl-1,3-butadiene contributing 34 ± 10%. The reaction is initiated by a barrierless addition of the phenyl radical to the terminal carbon atom of the 1,3-butadiene (C1/C4) to form a bound intermediate; the latter underwent hydrogen elimination from the terminal CH(2) group of the 1,3-butadiene molecule leading to 1-phenyl-trans-1,3-butadiene through a submerged barrier. The dominant product, 1,4-dihydronaphthalene, is formed via an isomerization of the adduct by ring closure and emission of the hydrogen atom from the phenyl moiety at the bridging carbon atom through a tight exit transition state located about 31 kJ mol(-1) above the separated products. The hydrogen atom was found to leave the decomposing complex almost parallel to the total angular momentum vector and perpendicularly to the rotation plane of the decomposing intermediate. The defacto barrierless formation of the 1,4-dihydronaphthalene molecule involving a single collision between a phenyl radical and 1,3-butadiene represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated counterparts in combustion and interstellar chemistry.

On the formation of phenyldiacetylene (C6H5CCCCH) and D5-phenyldiacetylene (C6D5CCCCH) studied under single collision conditions.

The crossed molecular beam reactions of the phenyl and D5-phenyl radical with diacetylene (C(4)H(2)) was studied under single collision conditions at a collision energy of 46 kJ mol(-1). The chemical dynamics were found to be indirect and initiated by an addition of the phenyl/D5-phenyl radical with its radical center to the C1-carbon atom of the diacetylene reactant. This process involved an entrance barrier of 4 kJ mol(-1) and lead to a long lived, bound doublet radical intermediate. The latter emitted a hydrogen atom directly or after a few isomerization steps via tight exit transition states placed 20-21 kJ mol(-1) above the separated phenyldiacetylene (C(6)H(5)CCCCH) plus atomic hydrogen products. The overall reaction was determined to be exoergic by about 49 ± 26 kJ mol(-1) and 44 ± 10 kJ mol(-1) as determined experimentally and computationally, thus representing a feasible pathway to the formation of the phenyldiacetylene molecule in combustion flames of hydrocarbon fuel.

Crossed beam reaction of phenyl and D5-phenyl radicals with propene and deuterated counterparts--competing atomic hydrogen and methyl loss pathways.

We conducted the crossed molecular beams reactions of the phenyl and D5-phenyl radicals with propylene together with its partially deuterated reactants at collision energies of ~45 kJ mol(-1) under single collision conditions. The scattering dynamics were found to be indirect and were mainly dictated by an addition of the phenyl radical to the sterically accessible CH(2) unit of the propylene reactant. The resulting doublet radical isomerized to multiple C(9)H(11) intermediates, which were found to be long-lived, decomposing in competing methyl group loss and atomic hydrogen loss pathways with the methyl group loss leading to styrene (C(6)H(5)C(2)H(3)) and the atomic hydrogen loss forming C(9)H(10) isomers cis/trans 1-phenylpropene (CH(3)CHCHC(6)H(5)) and 3-phenylpropene (C(6)H(5)CH(2)C(2)H(3)). Fractions of the methyl versus hydrogen loss channels of 68 ± 16% : 32 ± 10% were derived experimentally, which agrees nicely with RRKM theory. As the collision energy rises to 200 kJmol(-1), the contribution of the methyl loss channel decreases sharply to typically 25%; the decreased importance of the methyl group loss channel was also demonstrated in previous crossed beam experiments conducted at elevated collision energies of 130-193 kJ mol(-1). The presented work highlights the interesting differences of the branching ratios with rising collision energies in the reaction dynamics of phenyl radicals with unsaturated hydrocarbons related to combustion processes. The facility of forming styrene, a common molecule found in combustion against the elusiveness of forming the cyclic indane molecule demonstrates the need to continue to explore the potential surfaces through the combinative single collision experiment and electronic structure calculations.

Competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene.

We report new, detailed, femtosecond time-resolved photoelectron spectroscopy experiments and calculations investigating the competition between ultrafast internal conversion and ultrafast intersystem crossing in electronically and vibrationally excited benzene at the onset of "channel 3". Using different probe energies to record the total photoelectron yield as a function of pump-probe delay we are able to confirm that S(1), T(1) and T(2) electronic states are involved in the excited state dynamics. Time-resolved photoelectron spectroscopy measurements then allow us to unravel the evolution of the S(1), T(1) and T(2) components of the excited state population and, together with complementary quantum chemistry and quantum dynamics calculations, support our earlier proposal that ultrafast intersystem crossing competes with internal conversion (Chem. Phys. Lett., 2009, 469, 43).

Challenges in phenotype definition in the whole-genome era: multivariate models of memory and intelligence.

Refining phenotypes for the study of neuropsychiatric disorders is of paramount importance in neuroscience. Poor phenotype definition provides the greatest obstacle for making progress in disorders like schizophrenia, bipolar disorder, Attention Deficit/Hyperactivity Disorder (ADHD), and autism. Using freely available informatics tools developed by the Consortium for Neuropsychiatric Phenomics (CNP), we provide a framework for defining and refining latent constructs used in neuroscience research and then apply this strategy to review known genetic contributions to memory and intelligence in healthy individuals. This approach can help us begin to build multi-level phenotype models that express the interactions between constructs necessary to understand complex neuropsychiatric diseases. These results are available online through the http://www.phenowiki.org database. Further work needs to be done in order to provide consensus-building applications for the broadly defined constructs used in neuroscience research.

Literature Mapping with PubAtlas - extending PubMed with a 'BLASTing interface'.

PubAtlas (www.pubatlas.org) is a web service and standalone program providing literature maps for the biomedical research literature. It accepts user-defined sets of terms (PubMed queries) as input, and permits 'BLASTing' of one set against another: for all terms x and y in these sets, deriving the results of the pairwise intersections x AND y. This all vs. all capability extends PubMed with a literature analysis interface. Correspondingly, the basic form of literature map that PubAtlas provides for exploring associations among sets of terms is an interactive tabular display, in heatmap/microarray format.PubAtlas supports development of specialized lexica -- hierarchies of controlled terminology that can represent sets of related concepts or a 'user-defined query language'. PubAtlas also provides historical perspectives on the literature, with temporal query features that highlight historical patterns. Generally, it is a framework for extending the PubMed interface, and an extensible platform for producing interactive literature maps.

A collaborative knowledge base for cognitive phenomics.

The human genome project has stimulated development of impressive repositories of biological knowledge at the genomic level and new knowledge bases are rapidly being developed in a 'bottom-up' fashion. In contrast, higher-level phenomics knowledge bases are underdeveloped, particularly with respect to the complex neuropsychiatric syndrome, symptom, cognitive, and neural systems phenotypes widely acknowledged as critical to advance molecular psychiatry research. This gap limits informatics strategies that could improve both the mining and representation of relevant knowledge, and help prioritize phenotypes for new research. Most existing structured knowledge bases also engage a limited set of contributors, and thus fail to leverage recent developments in social collaborative knowledge-building. We developed a collaborative annotation database to enable representation and sharing of empirical information about phenotypes important to neuropsychiatric research (www.Phenowiki.org). As a proof of concept, we focused on findings relevant to 'cognitive control', a neurocognitive construct considered important to multiple neuropsychiatric syndromes. Currently this knowledge base tabulates empirical findings about heritabilities and measurement properties of specific cognitive task and rating scale indicators (n=449 observations). It is hoped that this new open resource can serve as a starting point that enables broadly collaborative knowledge-building, and help investigators select and prioritize endophenotypes for translational research.

Absorption and digestive tract metabolism of 2-hydroxy-4-methylthiobutanoic acid in lambs.

Anabolic availability of the hydroxyl methionine analog, 2-hydroxy-4-methylthiobutanoic acid (HMTBA), given as oral doses to lambs, was quantified both directly as appearance in the portal vein and as synthesis to Met by digestive tract tissues. Eight lambs, prepared with vascular catheters in the mesenteric and portal veins plus the aorta, received twice daily for 7 d either 0.46 g or 2 g of HMTBA. On d 7, [1-13C]HMTBA was supplied as 1 oral dose while [methyl-2H3]Met was infused into the jugular vein. Peak absorption as HMTBA occurred 70 to 90 min after the oral dose. All digestive tract tissues converted HMTBA to Met, equivalent to 24% of the Met provided by the diet for the larger HMTBA dose. Overall, total availability of HMBTA averaged 17.9% of the dose (range 10.6 to 27.9%), with 12.5% (range 7 to 22%) as absorbed HMBTA and the remainder as Met synthesized by digestive tract tissues. Release of 13CO2 into the portal vein accounted for another 23% of the dose. In all digestive tract tissues, the d-isomer was present in a smaller proportion than in the dose. In terms of whole-body kinetics, HMTBA loss from the plasma followed first-order kinetics, with a mean biological half-life of 76 min. Using this value, a simple model was devised to estimate HMTBA absorption based on peripheral plasma samples. When compared with direct measures of absorption, the model gave a slope of 0.81 (R2 = 0.68) and offers a practical means to test HMTBA availability to animals.

Hepatic metabolism of 2-hydroxy-4-methylthiobutyrate in growing lambs.

This study was undertaken to determine how, and where, 2-hydroxy-4-methylthiobutyrate (HMTBA) can augment Met metabolism in lambs. Four lambs (initial body weight of 50 kg, SE = 2, and 6 mo of age) prepared with catheters in the mesenteric, portal, hepatic, and jugular veins plus the aorta, were fed at 1.5x maintenance on a grass hay, barley, fish meal, molasses/pre-mix (5:3:1:1, as fed) diet, supplied as hourly meals. Lambs were infused for 10 h with [methyl-2H3]Met (0.11 mmol/h) in a jugular vein and p-aminohippurate into the mesenteric vein. From 1 h onwards, successive 3-h infusions of saline (control), 0.55 mg/min (3.67 micromol/min), and 4.44 mg/min (29.6 micromol/min) of HMTBA were also infused into the mesenteric vein. Plasma, sampled continuously, was collected every 20 min during the last 60 min of each infusion. All infused HMTBA was recovered at the portal vein with 25% extracted subsequently by the liver. Portal appearance of total Cys and Met was unaltered by HMTBA infusion, but net splanchnic appearance of Cys increased (0.04, 0.08, 0.23 mmol/h, SEM = 0.05), whereas Met decreased (0.14, -0.01, -0.21 mmol/h, SED = 0.05). Despite this, arterial Met increased (27.0, 30.7, 51.5 microM, SEM = 2.1) as did Met irreversible loss rate (27.6, 28.7, 40.1 micromol/h, SEM = 0.51), equivalent to 40% of the HMTBA reentering the plasma after conversion to Met. These data indicate that, in ruminants, HMTBA is probably converted to Met within peripheral tissues; that is, where the metabolic need for Met exists.

Absorption of 2-hydroxy-4-methylthiobutyrate and conversion to methionine in lambs.

Absorption and metabolism of the Met hydroxy analog 2-hydroxy-4-methylthiobutyrate (HMTBA) was examined using stable isotopes. In the first trial, Dl[1-13C]HMTBA was infused for 6 h (7.4 micromol/min) into the abomasum, and [2H3]Met was infused into the mesenteric vein, of 4 lambs prepared with vascular catheters across the splanchnic bed. Daily, lambs were offered 35 g of a mixed forage-concentrate feed/kg. Recovery of HMTBA at the portal vein was 87%, and of this, 63% bypassed the liver. In contrast, hepatic extraction of Met equaled or exceeded net absorption. Only small quantities of Met synthesized from HMTBA were exported from either the digestive tract or liver, but there was substantial and significant input from posthepatic tissues. In a second experiment, 3 of the lambs were killed following 4-h infusions of DL[1-13C]HMTBA and [2H3]Met with enrichments monitored in 15 tissues. Only kidney showed [1-13C]Met enrichment higher than plasma, which suggests that it must be a primary source of plasma Met derived from HMTBA. Based on comparison of plasma and intracellular [1-13C]:[2H3]Met enrichments, all tissues synthesized Met from HMTBA but to significantly different extents. The lowest values were for muscle, skin, brain, and lung; intermediate conversions occurred in rumen, omasum, abomasum, duodenum, jejunum, ileum, and cecum; and the greatest synthesis, equivalent to 22 to 24% of Met entry into cells, was observed for liver and kidney. Therefore, although liver and kidney both converted HMTBA to Met, it was retained by the former and exported by the latter. Under these experimental conditions, synthesis of Met from HMTBA completely eliminated use of dietary Met.

Gene transfer in the gastrointestinal tract.

The maximum in vivo transfer rate of plasmid pAMbeta1 in the gut was 0.03 transconjugant per recipient cell, and this rate could be simulated in vitro only by forced filter mating. Transfer was not detected in liquid culture matings. Our findings demonstrate that in vitro methods, such as forced filter mating and liquid mating, underestimate the in vivo rates of gene transfer.

Probiotics shown to change bacterial community structure in the avian gastrointestinal tract.

Culturing and molecular techniques were used to monitor changes in the bacterial flora of the avian gastrointestinal (GI) tract following introduction of genetically modified (GM) and unmodified probiotics. Community hybridization of amplified 16S ribosomal DNA demonstrated that the bacterial flora of the GI tract changed significantly in response to the probiotic treatments. The changes were not detected by culturing. Although both GM and non-GM strains of Enterococcus faecium NCIMB 11508 changed the bacterial flora of the chicken GI tract, they did so differently. Probing the community DNA with an Enterococcus faecalis-specific probe showed that the relative amount of E. faecalis in the total eubacterial population increased in the presence of the non-GM strain and decreased in the presence of the GM probiotic compared with the results obtained with an untreated control group.