Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period

Introduction

Neonatal calf diarrhea is a multifactorial condition that occurs in early life when calves are particularly susceptible to enteric infection and dysbiosis of the gut microbiome. Good calf health is dependent on successful passive transfer of immunity from the dam through colostrum. There are limited studies on the developing gut microbiota from birth to weaning in calves.

Methodology

Therefore, the objective of this study was to examine the effect of immune status and diarrheal incidence on the development of the fecal microbiota in Jersey (n = 22) and Holstein (n = 29) heifer calves throughout the pre-weaning period. Calves were hand-fed a colostrum volume equivalent to 8.5% of their birthweight, from either the calf's dam (n = 28) or re-heated mixed colostrum (≤2 cows, ≤1d; n = 23) within 2 h of birth. All calves were clinically assessed using a modified Wisconsin-Madison calf health scoring system and rectal temperature at day (d) 0, d7, d21, or disease manifestation (DM) and weaning (d83). Weights were recorded at d0, d21, and d83. Calf blood samples were collected at d7 for the determination of calf serum IgG (sIgG). Fecal samples were obtained at d7, d21/DM [mean d22 (SE 0.70)], and at weaning for 16S rRNA amplicon sequencing of the fecal microbiota. Data were processed in R using DADA2; taxonomy was assigned using the SILVA database and further analyzed using Phyloseq and MaAsLin 2.

Results and discussion

Significant amplicon sequence variants (ASVs) and calf performance data underwent a Spearman rank-order correlation test. There was no effect (p > 0.05) of colostrum source or calf breed on serum total protein. An effect of calf breed (p < 0.05) was observed on sIgG concentrations such that Holstein calves had 6.49 (SE 2.99) mg/ml higher sIgG than Jersey calves. Colostrum source and calf breed had no effect (p > 0.05) on health status or the alpha diversity of the fecal microbiota. There was a relationship between health status and time interaction (p < 0.001), whereby alpha diversity increased with time; however, diarrheic calves had reduced microbial diversity at DM. No difference (p > 0.05) in beta diversity of the microbiota was detected at d7 or d83. At the genus level, 33 ASVs were associated (adj.p < 0.05) with health status over the pre-weaning period.

The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm?

During protein evolution, some amino acid substitutions modulate protein function ("tuneability"). In most proteins, the tuneable range is wide and can be sampled by a set of protein variants that each contains multiple amino acid substitutions. In other proteins, the full tuneable range can be accessed by a set of variants that each contains a single substitution. Indeed, in some globular proteins, the full tuneable range can be accessed by the set of site-saturating substitutions at an individual "rheostat" position. However, in proteins with intrinsically disordered regions (IDRs), most functional studies-which would also detect tuneability-used multiple substitutions or small deletions. In disordered transcriptional activation domains (ADs), studies with multiple substitutions led to the "acidic exposure" model, which does not anticipate the existence of rheostat positions. In the few studies that did assess effects of single substitutions on AD function, results were mixed: the ADs of two full-length transcription factors did not show tuneability, whereas a fragment of a third AD was tuneable by single substitutions. In this study, we tested tuneability in the AD of full-length human class II transactivator (CIITA). Sequence analyses and experiments showed that CIITA's AD is an IDR. Functional assays of singly-substituted AD variants showed that CIITA's function was highly tuneable, with outcomes not predicted by the acidic exposure model. Four tested positions showed rheostat behavior for transcriptional activation. Thus, tuneability of different IDRs can vary widely. Future studies are needed to illuminate the biophysical features that govern whether an IDR is tuneable by single substitutions.

Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes

The functions of many proteins are associated with interconversions among conformational substates. However, these substates can be difficult to measure experimentally, and determining contributions from hydration changes can be especially difficult. Here, we assessed the use of pressure perturbations to sample the substates accessible to the Escherichia coli lactose repressor protein (LacI) in various liganded forms. In the presence of DNA, the regulatory domain of LacI adopts an Open conformation that, in the absence of DNA, changes to a Closed conformation. Increasing the simulation pressure prevented the transition from an Open to a Closed conformation, in a similar manner to the binding of DNA and anti-inducer, ONPF. The results suggest the hydration of specific residues play a significant role in determining the population of different LacI substates and that simulating pressure perturbation could be useful for assessing the role of hydration changes that accompany functionally-relevant amino acid substitutions.

Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems

Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH₄), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H₂ and CO₂), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH₄-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH₄ mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.

Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions

With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of ruminant livestock divergently ranked for enteric emissions. Recently, the residual methane emissions (RME) concept has been identified as the optimal phenotype for assessing the methanogenic potential of ruminant livestock due to the trait's independence from animal productivity but strong correlation with daily methane emissions. However, there is currently a dearth of data available on the bacterial and archaeal microbial communities residing in the rumens of animals divergently ranked for RME. Therefore, the objective of this study was to investigate the relationship between the rumen microbiota and RME in a population of finishing beef cattle. Methane emissions were estimated from individual animals using the GreenFeed Emissions Monitoring system for 21 days over a mean feed intake measurement period of 91 days. Residual methane emissions were calculated for 282 crossbred finishing beef cattle, following which a ∼30% difference in all expressions of methane emissions was observed between high and low RME ranked animals. Rumen fluid samples were successfully obtained from 268 animals during the final week of the methane measurement period using a trans-oesophageal sampling device. Rumen microbial DNA was extracted and subjected to 16S rRNA amplicon sequencing. Animals ranked as low RME had the highest relative abundances (P < 0.05) of lactic-acid-producing bacteria (Intestinibaculum, Sharpea, and Olsenella) and Selenomonas, and the lowest (P < 0.05) proportions of Pseudobutyrivibrio, Butyrivibrio, and Mogibacterium. Within the rumen methanogen community, an increased abundance (P < 0.05) of the genus Methanosphaera and Methanobrevibacter RO clade was observed in low RME animals. The relative abundances of both Intestinibaculum and Olsenella were negatively correlated (P < 0.05) with RME and positively correlated with ruminal propionate. A similar relationship was observed for the abundance of Methanosphaera and the Methanobrevibacter RO clade. Findings from this study highlight the ruminal abundance of bacterial genera associated with the synthesis of propionate via the acrylate pathway, as well as the methanogens Methanosphaera and members of the Methanobrevibacter RO clade as potential microbial biomarkers of the methanogenic potential of beef cattle.

Effect of divergence in residual methane emissions on feed intake and efficiency, growth and carcass performance, and indices of rumen fermentation and methane emissions in finishing beef cattle

Residual expressions of enteric emissions favor a more equitable identification of an animal's methanogenic potential compared with traditional measures of enteric emissions. The objective of this study was to investigate the effect of divergently ranking beef cattle for residual methane emissions (RME) on animal productivity, enteric emissions, and rumen fermentation. Dry matter intake (DMI), growth, feed efficiency, carcass output, and enteric emissions (GreenFeed emissions monitoring system) were recorded on 294 crossbred beef cattle (steers = 135 and heifers = 159; mean age 441 d (SD = 49); initial body weight (BW) of 476 kg (SD = 67)) at the Irish national beef cattle performance test center. Animals were offered a total mixed ration (77% concentrate and 23% forage; 12.6 MJ ME/kg of DM and 12% CP) ad libitum with emissions estimated for 21 d over a mean feed intake measurement period of 91 d. Animals had a mean daily methane emissions (DME) of 229.18 g/d (SD = 45.96), methane yield (MY) of 22.07 g/kg of DMI (SD = 4.06), methane intensity (MI) 0.70 g/kg of carcass weight (SD = 0.15), and RME 0.00 g/d (SD = 0.34). RME was computed as the residuals from a multiple regression model regressing DME on DMI and BW (R2 = 0.45). Animals were ranked into three groups namely high RME (>0.5 SD above the mean), medium RME (±0.5 SD above/below the mean), and low RME (>0.5 SD below the mean). Low RME animals produced 17.6% and 30.4% less (P < 0.05) DME compared with medium and high RME animals, respectively. A ~30% reduction in MY and MI was detected in low versus high RME animals. Positive correlations were apparent among all methane traits with RME most highly associated with (r = 0.86) DME. MY and MI were correlated (P < 0.05) with DMI, growth, feed efficiency, and carcass output. High RME had lower (P < 0.05) ruminal propionate compared with low RME animals and increased (P < 0.05) butyrate compared with medium and low RME animals. Propionate was negatively associated (P < 0.05) with all methane traits. Greater acetate:propionate ratio was associated with higher RME (r = 0.18; P < 0.05). Under the ad libitum feeding regime deployed here, RME was the best predictor of DME and only methane trait independent of animal productivity. Ranking animals on RME presents the opportunity to exploit interanimal variation in enteric emissions as well as providing a more equitable index of the methanogenic potential of an animal on which to investigate the underlying biological regulatory mechanisms.

Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20

Here, we perform structural, thermodynamic, and kinetics tests of the Kirkwood-Buff-derived force field, KBFF20, for peptides and proteins developed in the previous article. The physical/structural tests measure the ability of KBFF20 to capture the experimental J-couplings for small peptides, to keep globular monomeric and oligomeric proteins folded, and to produce the experimentally relevant expanded conformational ensembles of intrinsically disordered proteins. The thermodynamic-based tests probe KBFF20's ability to quantify the preferential interactions of sodium chloride around native β-lactoglobulin and urea around native lysozyme, to reproduce the melting curves for small helix- and sheet-based peptides, and to fold the small proteins Trp-cage and Villin. The kinetics-based tests quantify how well KBFF20 can match the experimental contact formation rates of small, repeat-sequence peptides of variable lengths and the rotational diffusion coefficients of globular proteins. The results suggest that KBFF20 is naturally able to reproduce properties of both folded and disordered proteins, which we attribute to the use of the Kirkwood-Buff theory as the foundation of the force field's development. However, we show that KBFF20 tends to lose some well-defined secondary structural elements and increases the percentage of coil regions, indicating that the perfect balance of all interactions remains elusive. Nevertheless, we argue that KBFF20 is an improvement over recently modified force fields that require ad hoc interventions to prevent the collapse of intrinsically disordered proteins.

Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20

A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis

Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency

Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = −0.53; solid, rho = −0.56) and Olsenella (solid, rho = −0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)

Plant based by-products (BP) produced from food and bioethanol industries are human inedible, but can be recycled into the global food chain by ruminant livestock. However, limited data is available on the methanogenesis potential associated with supplementing a solely BP formulated concentrate to a pastoral based diet. Therefore the objective of this in vitro study was to investigate the effects of BP inclusion rate (in a formulated concentrate) to a pasture based diet on dietary digestibility, rumen fermentation patterns, methane production and the prokaryotic microbial community composition. Diets consisted of perennial ryegrass and one of two supplementary concentrates, formulated to be isonitrogenous (16% CP) and isoenergetic (12.0 MJ/ME/kg), containing either 35% BP, barley and soybean meal (BP35) or 95% BP (BP95) offered on a 50:50 basis, however, starch, NDF and fat content varied. The BPs, included in equal proportions on a DM basis, were soyhulls, palm kernel expeller and maize dried distillers grains. The BP35 diet had greater (P < 0.05) digestibility of the chemical constituents DM, OM, CP, NDF, ADF. Greater total VFA production was seen in the BP35 diet (P < 0.05). Daily methane production (mmol/day; +22.7%) and methane output per unit of total organic matter digested (MPOMD; +20.8%) were greatest in the BP35 diet (P < 0.01). Dietary treatment influenced microbial composition (PERMANOVA; P = 0.023) with a greater relative abundance of Firmicutes (adj P < 0.01) observed in the BP35. The Firmicutes:Bacteroidetes ratio was significantly reduced in the BP95 diet (P < 0.01). The relative proportions of Proteobacteria (adj P < 0.01), Succinivibrionaceae (adj P < 0.03) and Succinivibrio (adj P = 0.053) increased in the BP95 diet. The abundance of Proteobacteria was found to be negatively associated with daily methane production (r_s, −0.71; P < 0.01) and MPOMD (r_s, −0.65; P < 0.01). Within Proteobacteria, the relationship of methane production was maintained with the mean abundance of Succinivibrio (r_s, −0.69; P < 0.01). The abundance of the Firmicutes phyla was found to be positively correlated with both daily methane production (r_s, 0.79; P < 0.001) and MPOMD (r_s, 0.75; P < 0.01). Based on in vitro rumen simulation data, supplementation of an exclusively BP formulated concentrate was shown to reduce daily methane output by promoting a favorable alteration to the rumen prokaryotic community.

P54 Formative test questions in neurology and neurosurgery

Objectives

To provide a formative educational test of knowledge that allows clinicians to measure themselves against their peers.

Design

Annual Neurosurgery and Neurology knowledge tests, supported by the ABN & SBNS, have been available since 2014 (NSurg) and 2017 (Neurol). The NSurg test requires all candidates to participate over 3 days, answers are available after the test whereas the Neurol formative questions are available over 6 weeks, answers are available immediately.

Subjects

There have been 821 first attempts at the formative questions; NSurg; 44, 63,187,143,164 and Neurol; 74, 146. Candidates are mostly from UK (NSurg 92%, Neurol 69%) and mostly specialty trainees (NSurg 98%, Neurol 63%).

Methods

The formative questions are delivered through the ebrain virtual learning platform, statistics are generated automatically. Proposed questions are written by candidates as ‘payment’ for doing the formative test.

Results

Mean Cronbach’s alpha was 87.3%. The mean score for the tests was 60.4% (Range 55.9%–77.9%). Feedback is voluntary: In 2018 17 feedback comments were received, 10 were unambiguously positive, 5 were mixed including criticism of one or more questions, 2 were judged to be neutral. Examples of feedback comments received this year included ‘Comprehensive exam that covers a wide range of topics’ and ‘This is of great value’.

Conclusions

This formative educational initiative has high internal consistency and solid feedback. Although set up differently, it is proving both valuable and popular in both specialties.

Classical harmonic model for the behavior of pure fluids at the critical point

We present a simple model to explain the limiting behavior of many thermodynamic properties of pure classical fluids as one approaches the critical point.

Experimental Investigation of Triplet Correlation Approximations for Fluid Water

Triplet correlations play a central role in our understanding of fluids and their properties. Of particular interest is the relationship between the pair and triplet correlations. Here we use a combination of Fluctuation Solution Theory and experimental pair radial distribution functions to investigate the accuracy of the Kirkwood Superposition Approximation (KSA), as given by integrals over the relevant pair and triplet correlation functions, at a series of state points for pure water using only experimental quantities. The KSA performs poorly, in agreement with a variety of other studies. Several additional approximate relationships between the pair and triplet correlations in fluids are also investigated and generally provide good agreement for the fluid thermodynamics for regions of the phase diagram where the compressibility is small. A simple power law relationship between the pair and triplet fluctuations is particularly successful for state points displaying low to moderately high compressibilities.

A Kirkwood-Buff derived force field for alkaline earth halide salts

The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX₂), where M = Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺ and X = Cl^-, Br^-, I^-, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

Peptide nanosponges designed for rapid uptake by leukocytes and neural stem cells

The structure of novel binary nanosponges consisting of (cholesterol-(K/D)_nDEVDGC)₃-trimaleimide units possessing a trigonal maleimide linker, to which either lysine (K)₂₀ or aspartic acid (D)₂₀ are tethered, has been elucidated by means of TEM. A high degree of agreement between these findings and structure predictions through explicit solvent and then coarse-grained molecular dynamics (MD) simulations has been found. Based on the nanosponges' structure and dynamics, caspase-6 mediated release of the model drug 5(6)-carboxyfluorescein has been demonstrated. Furthermore, the binary (DK20) nanosponges have been found to be virtually non-toxic in cultures of neural progenitor cells. It is of a special importance for the future development of cell-based therapies that DK20 nanosponges were taken up efficiently by leucocytes (WBC) in peripheral blood within 3 h of exposure. The percentage of live cells among the WBC was not significantly decreased by the DK20 nanosponges. In contrast to stem cell or leucocyte cell cultures, which have to be matched to the patient, autologous cells are optimal for cell-mediated therapy. Therefore, the nanosponges hold great promise for effective cell-based tumor targeting.

Nanosponges for drug delivery.

How Osmolytes Counteract Pressure Denaturation on a Molecular Scale

Life in the deep sea exposes enzymes to high hydrostatic pressure, which decreases their stability. For survival, deep sea organisms tend to accumulate various osmolytes, most notably trimethylamine N-oxide used by fish, to counteract pressure denaturation. However, exactly how these osmolytes work remains unclear. Here, a rigorous statistical thermodynamics approach is used to clarify the mechanism of osmoprotection. It is shown that the weak, nonspecific, and dynamic interactions of water and osmolytes with proteins can be characterized only statistically, and that the competition between protein-osmolyte and protein-water interactions is crucial in determining conformational stability. Osmoprotection is driven by a stronger exclusion of osmolytes from the denatured protein than from the native conformation, and water distribution has no significant effect on these changes at low osmolyte concentrations.

Epilepsy and Pregnancy: For healthy pregnancies and happy outcomes. Suggestions for service improvements from the Multispecialty UK Epilepsy Mortality Group

Between 2009 and 2012 there were 26 epilepsy-related deaths in the UK of women who were pregnant or in the first post-partum year. The number of pregnancy-related deaths in women with epilepsy (WWE) has been increasing. Expert assessment suggests that most epilepsy-related deaths in pregnancy were preventable and attributable to poor seizure control. While prevention of seizures during pregnancy is important, a balance must be struck between seizure control and the teratogenic potential of antiepileptic drugs (AEDs). A range of professional guidance on the management of epilepsy in pregnancy has previously been issued, but little attention has been paid to how optimal care can be delivered to WWE by a range of healthcare professionals. We summarise the findings of a multidisciplinary meeting with representation from a wide group of professional bodies. This focussed on the implementation of optimal pregnancy epilepsy care aiming to reduce mortality of epilepsy in mothers and reduce morbidity in babies exposed to AEDs in utero. We identify in particular -What stage to intervene - Golden Moments of opportunities for improving outcomes -Which Key Groups have a role in making change -When - 2020 vision of what these improvements aim to achieve. -How to monitor the success in this field We believe that the service improvement ideas developed for the UK may provide a template for similar initiatives in other countries.

Simulated pressure denaturation thermodynamics of ubiquitin

Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.

Atelectasis and mechanical ventilation mode during conservative oxygen therapy: A before-and-after study

PURPOSE

The purpose of the study is to assess the effect of a conservative oxygen therapy (COT) (target SpO2 of 90%-92%) on radiological atelectasis and mechanical ventilation modes.

MATERIALS AND METHODS

We conducted a secondary analysis of 105 intensive care unit patients from a pilot before-and-after study. The primary outcomes of this study were changes in atelectasis score (AS) of 555 chest radiographs assessed by radiologists blinded to treatment allocation and time to weaning from mandatory ventilation and first spontaneous ventilation trial (SVT).

RESULTS

There was a significant difference in overall AS between groups, and COT was associated with lower time-weighted average AS. In addition, in COT patients, change from mandatory to spontaneous ventilation or time to first SVT was shortened. After adjustment for baseline characteristics and interactions between oxygen therapy, radiological atelectasis, and mechanical ventilation management, patients in the COT group had significantly lower "best" AS (adjusted odds ratio, 0.28 [95% confidence interval {CI}, 0.12-0.66]; P=.003) and greater improvement in AS in the first 7 days (adjusted odds ratio, 0.42 [95% CI, 0.17-0.99]; P=.049). Moreover, COT was associated with significantly earlier successful weaning from a mandatory ventilation mode (adjusted hazard ratio, 2.96 [95% CI, 1.73-5.04]; P<.001) and with shorter time to first SVT (adjusted hazard ratio, 1.77 [95% CI, 1.13-2.78]; P=.013).

CONCLUSIONS

In mechanically ventilated intensive care unit patients, COT might be associated with decreased radiological evidence of atelectasis, earlier weaning from mandatory ventilation modes, and earlier first trial of spontaneous ventilation.

Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures

Kirkwood-Buff or Fluctuation Solution Theory can be used to provide experimental pair fluctuations, and/or integrals over the pair distribution functions, from experimental thermodynamic data on liquid mixtures. Here, this type of approach is used to provide triplet and quadruplet fluctuations, and the corresponding integrals over the triplet and quadruplet distribution functions, in a purely thermodynamic manner that avoids the use of structure factors. The approach is then applied to binary mixtures of water + methanol and benzene + methanol over the full composition range under ambient conditions. The observed correlations between the different species vary significantly with composition. The magnitude of the fluctuations and integrals appears to increase as the number of the most polar molecule involved in the fluctuation or integral also increases. A simple physical picture of the fluctuations is provided to help rationalize some of these variations.

Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for pure liquids

Fluctuation solution theory has provided an alternative view of many liquid mixture properties in terms of particle number fluctuations. The particle number fluctuations can also be related to integrals of the corresponding two body distribution functions between molecular pairs in order to provide a more physical picture of solution behavior and molecule affinities. Here, we extend this type of approach to provide expressions for higher order triplet and quadruplet fluctuations, and thereby integrals over the corresponding distribution functions, all of which can be obtained from available experimental thermodynamic data. The fluctuations and integrals are then determined using the International Association for the Properties of Water and Steam Formulation 1995 (IAPWS-95) equation of state for the liquid phase of pure water. The results indicate small, but significant, deviations from a Gaussian distribution for the molecules in this system. The pressure and temperature dependence of the fluctuations and integrals, as well as the limiting behavior as one approaches both the triple point and the critical point, are also examined.

Infinitely dilute partial molar properties of proteins from computer simulation

A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.

Theory and Simulation of Multicomponent Osmotic Systems

Most cellular processes occur in systems containing a variety of components many of which are open to material exchange. However, computer simulations of biological systems are almost exclusively performed in systems closed to material exchange. In principle, the behavior of biomolecules in open and closed systems will be different. Here, we provide a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the Kirkwood-Buff (KB) theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly(2) and Gly(3) in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. In addition, KB theory is used to help rationalize the aggregation properties of the solutes. Here one observes that the picture of solute association described by the KB integrals, which are directly related to the solution thermodynamics, and that provided by more physical clustering approaches are different. It is argued that the combination of KB theory and simulation data provides a simple and powerful tool for the analysis of complex multicomponent open and closed systems.

Flexible connection of the N-terminal domain in ClpB modulates substrate binding and the aggregate reactivation efficiency

ClpB reactivates aggregated proteins in cooperation with DnaK/J. The ClpB monomer contains two nucleotide-binding domains (D1, D2), a coiled-coil domain, and an N-terminal domain attached to D1 with a 17-residue-long unstructured linker containing a Gly-Gly motif. The ClpB-mediated protein disaggregation is linked to translocation of substrates through the central channel in the hexameric ClpB, but the events preceding the translocation are poorly understood. The N-terminal domains form a ring surrounding the entrance to the channel and contribute to the aggregate binding. It was suggested that the N-terminal domain's mobility that is maintained by the unstructured linker might control the efficiency of aggregate reactivation. We produced seven variants of ClpB with modified sequence of the N-terminal linker. To increase the linker's conformational flexibility, we inserted up to four Gly next to the GG motif. To decrease the linker's flexibility, we deleted the GG motif and converted it into GP and PP. We found that none of the linker modifications inhibited the basal ClpB ATPase activity or its capability to form oligomers. However, the modified linker ClpB variants showed lower reactivation rates for aggregated glucose-6-phosphate dehydrogenase and firefly luciferase and a lower aggregate-binding efficiency than wt ClpB. We conclude that the linker does not merely connect the N-terminal domain, but it supports the chaperone activity of ClpB by contributing to the efficiency of aggregate binding and disaggregation. Moreover, our results suggest that selective pressure on the linker sequence may be crucial for maintaining the optimal efficiency of aggregate reactivation by ClpB.

Management of suspected viral encephalitis in adults--Association of British Neurologists and British Infection Association National Guidelines

In the 1980s the outcome of patients with herpes simplex encephalitis was shown to be dramatically improved with aciclovir treatment. Delays in starting treatment, particularly beyond 48 h after hospital admission, are associated with a worse prognosis. Several comprehensive reviews of the investigation and management of encephalitis have been published. However, their impact on day-to day clinical practice appears to be limited. The emergency management of meningitis in children and adults was revolutionised by the introduction of a simple algorithm as part of management guidelines. In February 2008 a group of clinicians met in Liverpool to begin the development process for clinical care guidelines based around a similar simple algorithm, supported by an evidence base, whose implementation is hoped would improve the management of patients with suspected encephalitis.

Genetic epilepsy with febrile seizures plus: definite and borderline phenotypes

Generalised epilepsy with febrile seizures plus (GEFS+) is the most studied familial epilepsy syndrome. However, characteristics of UK families have not previously been reported. Among the first 80 families recruited to our families study, four broad subphenotypes were identified: families with classical GEFS+; families with borderline GEFS+; families with unclassified epilepsy; and families with an alternative syndromal diagnosis. Borderline GEFS+ families shared many characteristics of classical GEFS+ families-such as prominent febrile seizures plus and early onset febrile seizures-but included more adults with focal epilepsies (rather than the idiopathic generalised epilepsies predominating in GEFS+) and double the prevalence of migraine. Thus the authors believe that a novel and robust familial epilepsy phenotype has been identified. Subcategorising families with epilepsy is helpful in targeting both clinical and research resources. Most families with GEFS+ have no identified causal mutation, and so predicting genetic homogeneity by identifying endophenotypes becomes more important.

Local fluctuations in solution mixtures

An extension of the traditional Kirkwood-Buff (KB) theory of solutions is outlined which provides additional fluctuating quantities that can be used to characterize and probe the behavior of solution mixtures. Particle-energy and energy-energy fluctuations for local regions of any multicomponent solution are expressed in terms of experimentally obtainable quantities, thereby supplementing the usual particle-particle fluctuations provided by the established KB inversion approach. The expressions are then used to analyze experimental data for pure water over a range of temperatures and pressures, a variety of pure liquids, and three binary solution mixtures - methanol and water, benzene and methanol, and aqueous sodium chloride. In addition to providing information on local properties of solutions it is argued that the particle-energy and energy-energy fluctuations can also be used to test and refine solute and solvent force fields for use in computer simulation studies.

Fluctuation theory of molecular association and conformational equilibria

General expressions relating the effects of pressure, temperature, and composition on solute association and conformational equilibria using the fluctuation theory of solutions are provided. The expressions are exact and can be used to interpret experimental or computer simulation data for any multicomponent mixture involving molecules of any size and character at any composition. The relationships involve particle-particle, particle-energy, and energy-energy correlations within local regions in the vicinity of each species involved in the equilibrium. In particular, it is demonstrated that the results can be used to study peptide and protein association or aggregation, protein denaturation, and protein-ligand binding. Exactly how the relevant fluctuating properties may be obtained from experimental or computer simulation data are also outlined. It is shown that the enthalpy, heat capacity, and compressibility differences associated with the equilibrium process can, in principle, be obtained from a single simulation. Fluctuation based expressions for partial molar heat capacities, thermal expansions, and isothermal compressibilities are also provided.

A Kirkwood-Buff force field for the aromatic amino acids

In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides

A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide solutions (MX), where M = Li(+), Na(+), K(+), Rb(+), Cs(+) and X = F(-), Cl(-), Br(-), I(-), and their interactions with biomolecules. The models are specifically designed to reproduce the experimental Kirkwood-Buff integrals, and thereby the solution salt activities, as a function of salt concentration. Additionally, we demonstrate that these models reasonably reproduce other experimental properties including ion diffusion constants, dielectric decrements, and the excess heats of mixing. The parameters are developed by considering the properties of aqueous NaX and MCl solutions using a previously established model for NaCl. Transferability of the parameters to other salts is then established by the successful simulation of additional aqueous salt solutions, KI and CsBr, not originally included in the parameterization procedure.

Kirkwood-Buff integrals for ideal solutions

The Kirkwood-Buff (KB) theory of solutions is a rigorous theory of solution mixtures which relates the molecular distributions between the solution components to the thermodynamic properties of the mixture. Ideal solutions represent a useful reference for understanding the properties of real solutions. Here, we derive expressions for the KB integrals, the central components of KB theory, in ideal solutions of any number of components corresponding to the three main concentration scales. The results are illustrated by use of molecular dynamics simulations for two binary solutions mixtures, benzene with toluene, and methanethiol with dimethylsulfide, which closely approach ideal behavior, and a binary mixture of benzene and methanol which is nonideal. Simulations of a quaternary mixture containing benzene, toluene, methanethiol, and dimethylsulfide suggest this system displays ideal behavior and that ideal behavior is not limited to mixtures containing a small number of components.

The effect of urea on the morphology of NaCl crystals: A combined theoretical and simulation study

It has been known for over a century that the presence of cosolvents such as urea and formamide can alter the morphology of NaCl crystals grown from solution. To help understand this effect we have been developing a theoretical approach based on the Kirkwood-Buff (KB) theory of solutions, and have combined this with computer simulations of the interation of urea with different crystal faces of NaCl. In this way one can predict the effect of urea on the thermodynamic stability of different NaCl faces, with atomic level detail provided by the simulations. We observe that urea is preferentially excluded from 100 and 111 crystal faces, but is less excluded from 111 faces which present chloride ions at the surface. The results indicate that the 111 face is stabilized in urea solutions and promotes the formation of octahedral over cubic NaCl crystals. The approach is totally general and can be applied to understand a variety of interfacial properties. Furthermore, we apply KB theory to study several other issues regarding the simulation of crystal growth.

Developing Force Fields from the Microscopic Structure of Solutions

We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach.

Kirkwood-Buff theory of molecular and protein association, aggregation, and cellular crowding

An analysis of the effect of a cosolvent on the association of a solute in solution using the Kirkwood-Buff theory of solutions is presented. The approach builds on the previous results of Ben-Naim by extending the range of applicability to include any number of components at finite concentrations in both closed and semiopen systems. The derived expressions, which are exact, provide a foundation for the analysis and rationalization of cosolvent effects on molecular and biomolecular equilibria including protein association, aggregation, and cellular crowding. A slightly different view of cellular crowding is subsequently obtained. In particular, it is observed that the addition of large cosolvents still favors the associated form even when traditional excluded volume effects are absent.

Comment on "Can existing models quantitatively describe the mixing behavior of acetone with water" [J. Chem. Phys. 130, 124516 (2009)]

A recent publication indicated that simulations of acetone-water mixtures using the KBFF model for acetone indicate demixing at mole fractions less than 0.28 of acetone, in disagreement with experiment and two previously published studies. Here, we indicate some inconsistancies in the current study which could help to explain these differences.

A Kirkwood-Buff derived force field for thiols, sulfides, and disulfides

A force field has been developed for molecular simulations of methanethiol, dimethyl sulfide, and dimethyl disulfide mixtures. The force field specifically attempts to balance the solvation and self-association of these solutes in solution mixtures with methanol. The force field is based on the Kirkwood-Buff (KB) theory of solutions and is parametrized using the KB integrals obtained from the experimental activity coefficients for the solution mixtures. The transferability of the force field was tested and confirmed by the accurate prediction of the activity coefficients for methanethiol/dimethyl sulfide solutions, which were not used in the initial parametrization of the force fields. The ideality of this latter solution is excellently reproduced. The applicability of the force field to simulations in water was corroborated with a reasonably accurate prediction for the low solubility of dimethyl sulfide in water. The aggregation of methanol molecules at low methanol mole fractions displayed by all the mixtures is reproduced and further analyzed.