Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements

Site specific incorporation of molecular probes such as fluorescent- and nitroxide spin-labels into biomolecules, and subsequent analysis by Förster resonance energy transfer (FRET) and double electron-electron resonance (DEER) can elucidate the distance and distance-changes between the probes. However, the probes have an intrinsic conformational flexibility due to the linker by which they are conjugated to the biomolecule. This property minimizes the influence of the label side chain on the structure of the target molecule, but complicates the direct correlation of the experimental inter-label distances with the macromolecular structure or changes thereof. Simulation methods that account for the conformational flexibility and orientation of the probe(s) can be helpful in overcoming this problem. We performed distance measurements using FRET and DEER and explored different simulation techniques to predict inter-label distances using the Rpo4/7 stalk module of the M. jannaschii RNA polymerase. This is a suitable model system because it is rigid and a high-resolution X-ray structure is available. The conformations of the fluorescent labels and nitroxide spin labels on Rpo4/7 were modeled using in vacuo molecular dynamics simulations (MD) and a stochastic Monte Carlo sampling approach. For the nitroxide probes we also performed MD simulations with explicit water and carried out a rotamer library analysis. Our results show that the Monte Carlo simulations are in better agreement with experiments than the MD simulations and the rotamer library approach results in plausible distance predictions. Because the latter is the least computationally demanding of the methods we have explored, and is readily available to many researchers, it prevails as the method of choice for the interpretation of DEER distance distributions

Integrating Functional and Diffusion Magnetic Resonance Imaging for Analysis of Structure-Function Relationship in the Human Language Network

The capabilities of magnetic resonance imaging (MRI) to measure structural and functional connectivity in the human brain have motivated growing interest in characterizing the relationship between these measures in the distributed neural networks of the brain. In this study, we attempted an integration of structural and functional analyses of the human language circuits, including Wernicke's (WA), Broca's (BA) and supplementary motor area (SMA), using a combination of blood oxygen level dependent (BOLD) and diffusion tensor MRI.Functional connectivity was measured by low frequency inter-regional correlations of BOLD MRI signals acquired in a resting steady-state, and structural connectivity was measured by using adaptive fiber tracking with diffusion tensor MRI data. The results showed that different language pathways exhibited different structural and functional connectivity, indicating varying levels of inter-dependence in processing across regions. Along the path between BA and SMA, the fibers tracked generally formed a single bundle and the mean radius of the bundle was positively correlated with functional connectivity. However, fractional anisotropy was found not to be correlated with functional connectivity along paths connecting either BA and SMA or BA and WA. for use in diagnosing and determining disease progression and recovery

On the large-time behaviour of affine Volterra processes

We show the existence of a stationary measure for a class of multidimensional stochastic Volterra systems of affine type. These processes are in general not Markovian, a shortcoming which hinders their large-time analysis. We circumvent this issue by lifting the system to a measure-valued stochastic PDE introduced by Cuchiero and Teichmann, whence we retrieve the Markov property. Leveraging on the associated generalised Feller property, we extend the Krylov-Bogoliubov theorem to this infinite-dimensional setting and thus establish an approach to the existence of invariant measures. We present concrete examples, including the rough Heston model from Mathematical Finance.First author draf

Intramuscular fat in the 'longissimus' muscle is reduced in lambs from sires selected for leanness

Selection for lean growth through Australian Sheep Breeding Values (ASBVs) for post weaning weight (PWWT), eye muscle depth (PEMD) and c-site fat depth (PFAT) raises concerns regarding declining intramuscular fat (IMF) levels. Reducing PFAT decreased IMF by 0.84% for Terminal sired lambs. PEMD decreased IMF by 0.18% across all sire types. Female lambs had higher IMF levels and this was unexplained by total carcass fatness. The negative phenotypic association between measures of muscling (shortloin muscle weight, eye muscle area) and IMF, and positive association between fatness and IMF, was consistent with other literature. Hot carcass weight increased IMF by 2.08% between 12 and 40. kg, reflective of development of IMF as lambs approach maturity. Selection objectives with low PFAT sires will reduce IMF, however the lower impact of PEMD and absence of a PWWT effect, will enable continued selection for lean growth without influencing IMF. Alternatively, the negative impact of PFAT could be off-set by inclusion of an IMF ASBV

Associations of sire estimated breeding values and objective meat quality measurements with sensory scores in Australian lamb

The impact of selecting for lean meat yield using breeding values for increased eye muscle depth (PEMD) and decreased fat depth (PFAT) on the consumer acceptance of lamb meat was evaluated. Consumer sensory scores (tenderness, juiciness, flavour, odour, overall liking) were obtained for the longissimus lumborum (loin) and semimembranosus (topside) muscles of 1471 lambs. On average loin samples were more acceptable for consumers. Sensory scores increased with higher IMF levels, with lower shear force levels, and when animals were younger and less muscular. Increasing PEMD decreased tenderness, overall liking and flavour scores in both muscles, and decreasing PFAT reduced tenderness within the loin samples only. This negative impact of PEMD and PFAT is not solely driven through the phenotypic impact of IMF and shear force on sensory scores. Our results confirm the growing concerns that selecting for lean meat yield would reduce consumer eating quality, and highlight that careful monitoring of selection programmes is needed to maintain lamb eating quality

Genetic Parameters for Eating Quality Traits of Australian Lamb

Genetic parameters were estimated for 5 sensory (overall liking, tenderness, juiciness, flavour and liking of odour) and 2 objective eating quality (EQ) traits (intramuscular fat, IMF, and shear force, SF), measured on loin and topside meat cuts (except IMF) produced by progeny from the Information Nucleus of the CRC for Sheep Industry Innovation. Heritabilities for sensory traits were low to moderate for loin and moderate to high for topside cuts. Loin IMF was highly heritable while SF was moderately heritable in both cuts. Genetic correlations among the sensory EQ traits were all positive and high (0.72-1.00). Genetic correlations between loin IMF and sensory traits were moderately positive and lowly positive for loin and topside respectively. SF had stronger, negative correlations with sensory EQ traits in the topside than in the loin. Overall liking may be improved more so through selection on IMF in the loin and SF in the topside

Genetic and production factors that influence the content of intramuscular fat in the meat of prime lambs

Consumers are showing an increasing demand for juicy, flavoursome and tender meat, but in parallel are seeking lower fat, healthier food options. Intramuscular fat (IMF) has an important impact on palatability due to its specific contribution to juiciness and flavour and has been shown to contribute 10-15% of the variance in palatability (Dikeman, 1987). This can be compromised if the fat content is less than 3%, but is enhanced as IMF levels increase from 3-6% (Savell and Cross, 1988). Lamb contains about 4-5% IMF (Pethick et al., 2005), and studies have demonstrated that this is the level required to achieve consumer satisfaction (Hopkins et al., 2006). In recent years, increasing selection for lean growth has been linked to a decline in IMF level with subsequent detrimental effects on meat eating quality (Pethick et al., 2005). Thus maintaining sufficient levels in lamb meat is important to ensure the sensory appeal for consumers. The objectives of this study were to estimate the levels of IMF of slaughter progeny representing diverse genetic backgrounds and production systems, and to test the effect of genetic and non-genetic factors that affect IMF levels in prime lambs

Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX

Structure determination remains a challenge for many biologically important proteins. In particular, proteins that adopt multiple conformations often evade crystallization in all biologically relevant states. Although computational de novo protein folding approaches often sample biologically relevant conformations, the selection of the most accurate model for different functional states remains a formidable challenge, in particular, for proteins with more than about 150 residues. Electron paramagnetic resonance (EPR) spectroscopy can obtain limited structural information for proteins in well-defined biological states and thereby assist in selecting biologically relevant conformations. The present study demonstrates that de novo folding methods are able to accurately sample the folds of 192-residue long soluble monomeric Bcl-2-associated X protein (BAX). The tertiary structures of the monomeric and homodimeric forms of BAX were predicted using the primary structure as well as 25 and 11 EPR distance restraints, respectively. The predicted models were subsequently compared to respective NMR/X-ray structures of BAX. EPR restraints improve the protein-size normalized root-mean-square-deviation (RMSD100) of the most accurate models with respect to the NMR/crystal structure from 5.9 Å to 3.9 Å and from 5.7 Å to 3.3 Å, respectively. Additionally, the model discrimination is improved, which is demonstrated by an improvement of the enrichment from 5% to 15% and from 13% to 21%, respectively