Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.

Markov state models (MSMs) are quantitative models of protein dynamics that are useful for uncovering the structural fluctuations that proteins undergo, as well as the mechanisms of these conformational changes. Given the enormity of conformational space, there has been ongoing interest in identifying a small number of states that capture the essential features of a protein. Generally, this is achieved by making assumptions about the properties of relevant features-for example, that the most important features are those that change slowly. An alternative strategy is to keep as many degrees of freedom as possible and subsequently learn from the model which of the features are most important. In these larger models, however, traditional approaches quickly become computationally intractable. In this paper, we present enspara, a library for working with MSMs that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods. This includes ragged arrays for minimizing memory requirements, message passing interface-parallelized implementations of compute-intensive operations, and a flexible framework for model construction and analysis.

Effects of trace mineral amount and source on aspects of oxidative metabolism and responses to intramammary lipopolysaccharide challenge in midlactation dairy cows.

Trace minerals have important roles in immune function and oxidative metabolism; however, little is known about the relationships between supplementation level and source with outcomes in dairy cattle. Multiparous Holstein cows (n=48) beginning at 60 to 140 days in milk were utilized to determine the effects of trace mineral amount and source on aspects of oxidative metabolism and responses to intramammary lipopolysaccharide (LPS) challenge. Cows were fed a basal diet meeting National Research Council (NRC) requirements except for no added zinc (Zn), copper (Cu) or manganese (Mn). After a 4-week preliminary period, cows were assigned to one of four topdress treatments in a randomized complete block design with a 2×2 factorial arrangement of treatments: (1) NRC inorganic (NRC levels using inorganic (sulfate-based) trace mineral supplements only); (2) NRC organic (NRC levels using organic trace mineral supplements (metals chelated to 2-hydroxy-4-(methythio)-butanoic acid); (3) commercial inorganic (approximately 2×NRC levels using inorganic trace mineral supplements only; and (4) commercial organic (commercial levels using organic trace mineral supplements only). Cows were fed the respective mineral treatments for 6 weeks. Treatment effects were level, source and their interaction. Activities of super oxide dismutase and glutathione peroxidase in erythrocyte lysate and concentrations of thiobarbituric acid reactive substances (TBARS) and total antioxidant capacity (TAC) in plasma were measured as indices of oxidative metabolism. Effects of treatment on those indices were not significant when evaluated across the entire experimental period. Plasma immunoglobulin G level was higher in cows supplemented with organic trace minerals over the entire treatment period; responses assessed as differences of before and after Escherichia coli J5 bacterin vaccination at the end of week 2 of treatment period were not significant. Cows were administered an intramammary LPS challenge during week 5; during week 6 cows fed commercial levels of Zn, Cu and Mn tended to have higher plasma TAC and cows fed organic sources had decreased plasma TBARS. After the LPS challenge, the extent and pattern of response of plasma cortisol concentrations and clinical indices (rectal temperature and heart rate) were not affected by trace mineral level and source. Productive performance including dry matter intake and milk yield and composition were not affected by treatment. Overall, results suggest that the varying level and source of dietary trace minerals do not have significant short-term effects on oxidative metabolism indices and clinical responses to intramammary LPS challenge in midlactation cows.

How to Run FAST Simulations.

Molecular dynamics (MD) simulations are a powerful tool for understanding enzymes' structures and functions with full atomistic detail. These physics-based simulations model the dynamics of a protein in solution and store snapshots of its atomic coordinates at discrete time intervals. Analysis of the snapshots from these trajectories provides thermodynamic and kinetic properties such as conformational free energies, binding free energies, and transition times. Unfortunately, simulating biologically relevant timescales with brute force MD simulations requires enormous computing resources. In this chapter we detail a goal-oriented sampling algorithm, called fluctuation amplification of specific traits, that quickly generates pertinent thermodynamic and kinetic information by using an iterative series of short MD simulations to explore the vast depths of conformational space.

Meta-analysis of lactation performance in dairy cows receiving supplemental dietary methionine sources or postruminal infusion of methionine.

The objectives of our study were to evaluate the productive response to methionine supplementation in lactating dairy cows and to define a relationship between metabolizable Met (MP Met) intake and production. A database of 64 papers meeting the selection criteria was developed evaluating postruminally infused dl-methionine (9 papers with 18 control diets and 35 treatment comparisons), 2-hydroxy-4-methylthio butanoic acid (HMTBa) provided as either a liquid or Ca salt form (17 papers with 34 control diets and 46 treatment comparisons), Mepron (Evonik Industries, Essen, Germany; 18 papers with 35 control diets and 42 treatment comparisons), and Smartamine (Adisseo Inc., Antony, France; 20 papers with 30 control diets and 39 treatment comparisons). Dietary ingredients and their accompanying nutritional compositions as described in the reports were entered into the Cornell-Penn-Miner software to model the diets and to predict nutrients that were not reported in the original publication. Data were analyzed using a weighted analysis of response to supplementation compared with the intraexperiment control, as well as through a regression analysis to changing dietary MP Met. Data included in the analysis were from experiments published between 1970 and 2011 with cows supplemented with between 3.5 and 67.9 g of Met or its equivalent from HMTBa. Cows supplemented with Smartamine consumed more, whereas cows supplemented with Mepron consumed less DM compared with controls. Milk yield did not significantly respond to Met supplementation, although it tended to increase for cows supplemented with HMTBa and Mepron. Milk protein yield was increased due to supplementation from all sources or from infusion, and protein concentration was greater for all supplements or infusion of dl-Met, except for cows supplemented with HMTBa. Irrespective of Met source, milk protein yield increased 2.23 g of protein/g of MP Met until reaching the breakpoint. Milk fat yield was increased for Mepron and HMTBa, whereas milk fat concentration was increased for infused dl-Met and for cows supplemented with HMTBa. Based on regression analysis, response of milk fat yield to Met supplementation was not different for infused dl-Met, Mepron, and Smartamine (1.87 g of fat/g of MP Met), whereas the response to HMTBa was significantly greater at 5.38 g of fat/g of MP Met.

Fibrolytic enzymes and parity effects on feeding behavior, salivation, and ruminal pH of lactating dairy cows.

Four multiparous and four primiparous lactating dairy cows fitted with ruminal cannulas were used in a duplicated 4 x 4 Latin square design to study the effects of parity and inclusion of a fibrolytic enzyme product (Agribrands International, St. Louis, MO) on feeding and chewing behavior, salivation, and ruminal pH. Diets consisting of rolled barley, barley silage, and alfalfa haylage (55% forage, DM basis) differed in enzyme application: 1) control, 2) enzyme applied to concentrate (45% of TMR), 3) enzyme applied to supplement (4% of TMR), and enzyme applied to a premix (0.2% of TMR). Enzyme supplementation did not alter daily time spent eating or ruminating, but when enzymes were added to the ration daily, saliva production increased, with no difference among enzyme application treatments. Multiparous cows consumed a greater amount of feed, but spent a similar amount of time eating, compared to primiparous cows. Primiparous cows had shorter ruminating episodes, resulting in lower daily ruminating time compared with multiparous cows. Primiparous cows had lower daily saliva output compared with multiparous cows. These results indicate that application of this fibrolytic enzyme product did not alter the physical structure of the feed, as measured by feeding and chewing variables. The increase in total saliva production observed in cows fed enzyme-supplemented diets may be attributed to a physiological response to compensate for the increase in fermentation products during digestion. The increased intake for multiparous cows is attributed to increased eating rate and not to increased time spent eating. The higher DMI of multiparous cows resulted in increased rumination time needed to process the additional feed and increased salivation to buffer the greater production of VFA.

The proportion of the diet to which fibrolytic enzymes are added affects nutrient digestion by lactating dairy cows.

Eight lactating Holstein cows, four with ruminal cannulas, were used in a duplicated 4 x 4 Latin square design to investigate a fibrolytic enzyme product characterized by xylanase and cellulase activities (Promote N.E.T. Agribrands International, St. Louis, MO). The diet consisted of concentrate containing rolled barley and supplement, barley silage and alfalfa haylage (55% to 45% DM basis, forage to concentrate ratio) and differed in enzyme application: 1) control, 2) enzyme applied to concentrate (45% of TMR), 3) enzyme applied to supplement (4% of TMR), and 4) enzyme applied to premix (0.2% of TMR). All diets that were supplemented with the enzyme product delivered about 1.0 grams per cow per day. Digestibility of OM, NDF and ADF in the total tract was increased in comparison to the control when enzymes were added to the entire concentrate. Enzyme treatments that were applied to a smaller portion of the diet showed only numerical increases in digestibility over the control. However, there was an increase in microbial N synthesis for cows fed enzymes added to the premix. The effects of enzyme supplementation on milk production and composition were not statistically significant, but cows receiving the enzyme product added to the concentrate had a numerically higher FCM compared to the control cows. These results indicate that enzyme supplementation increases total tract digestibility of organic matter and fiber. The proportion of the diet to which the enzyme is applied must be maximized to ensure a beneficial response.

Analysis of a mutant exhibiting conditional sorting to dense core secretory granules in Tetrahymena thermophila.

The formation of dense core granules (DCGs) requires both the sorting of granule contents from other secretory proteins and a postsorting maturation process. The Tetrahymena thermophila strain SB281 fails to synthesize DCGs, and previous analysis suggested that the defect lay at or near the sorting step. Because this strain represents one of the very few mutants in this pathway, we have undertaken a more complete study of the phenotype. Genetic epistasis analysis places the defect upstream of those in two other characterized Tetrahymena mutants. Using immunofluorescent detection of granule content proteins, as well as GFP tagging, we describe a novel cytoplasmic compartment to which granule contents can be sorted in growing SB281 cells. Cell fusion experiments indicate that this compartment is not a biosynthetic intermediate in DCG synthesis. Sorting in SB281 is strongly conditional with respect to growth. When cells are starved, the storage compartment is degraded and de novo synthesized granule proteins are rapidly secreted. The mutation in SB281 therefore appears to affect DCG synthesis at the level of both sorting and maturation.

The gain-of-function Arabidopsis acd6 mutant reveals novel regulation and function of the salicylic acid signaling pathway in controlling cell death, defenses, and cell growth.

We isolated a dominant gain-of-function Arabidopsis mutant, accelerated cell death 6 (acd6), with elevated defenses, patches of dead and enlarged cells, reduced stature, and increased resistance to Pseudomonas syringae. The acd6-conferred phenotypes are suppressed by removing a key signaling molecule, salicylic acid (SA), by using the nahG transgene, which encodes SA hydroxylase. This suppression includes phenotypes that are not induced by application of SA to wild-type plants, indicating that SA acts with a second signal to cause many acd6-conferred phenotypes. acd6-nahG plants show hyperactivation of all acd6-conferred phenotypes after treatment with a synthetic inducer of the SA pathway, benzo(1,2, 3)thiadiazole-7-carbothioic acid (BTH), suggesting that SA acts with and also modulates the levels and/or activity of the second defense signal. acd6 acts partially through a NONEXPRESSOR OF PR 1 (NPR1) gene-independent pathway that activates defenses and confers resistance to P. syringae. Surprisingly, BTH-treated acd6-nahG plants develop many tumor-like abnormal growths, indicating a possible role for SA in modulating cell growth.