Protein Function Analysis through Machine Learning.

Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein-ligand binding, including allosteric effects, protein-protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.

Physical Inaccessibility of a Resistant Starch Shifts Mouse Gut Microbiota to Butyrogenic Firmicutes.

SCOPE: Resistant starch (RS) is utilized by Gram-negative Bacteroidetes through a starch utilization system (Sus), which requires physical attachment of the bacteria to the substrate. Gram-positive Firmicutes, which include butyrate producers, utilize RS by other mechanisms, such as amylosomes and secreted amylases/glucoamylases. It has been previously shown that fabricated RS [alginate-based starch-entrapped microspheres (SM)] increases butyrate in in vitro human fecal fermentation and was slow fermenting. It has been hypothesized that in vivo SM would disfavor Bacteroidetes and promote Firmicutes, leading to an increase in butyrate production. METHODS AND RESULTS: A C57BL/6J mouse model is used to test type 2 RS (RS2, raw potato) and SM for SCFAs and fecal microbial community structure. Feeding SM for 2 weeks results in 2.4 times higher mol% butyrate in the mouse distal gut than RS2. SM reduces relative abundance of Bacteroidetes and increases Firmicutes in fecal samples at the end of the 2-week feeding. This phylum-level taxonomic shift is not observed in animals fed RS2. CONCLUSION: Through an approach to understand bacterial requirements related to starch utilization, a designed fiber type favors butyrogenic Firmicutes bacteria and provides higher mol% butyrate in the distal gut with potential benefit as an anti-inflammatory agent and to improve gut barrier function.

Elevated propionate and butyrate in fecal ferments of hydrolysates generated by oxalic acid treatment of corn bran arabinoxylan.

Previous work in our laboratory showed that alkali-solubilized corn arabinoxylan (CAX) has a slow initial, but later complete, in vitro human fecal fermentation. CAX and a moderately high molecular weight hydrolysate (CH) were propiogenic, and produced low levels of butyrate. Here, we show that oxalic acid-generated hydrolysates from CAX, which include a large xylooligosaccharide, and free arabinose fractions, increased short chain fatty acid (SCFA) production, which included relatively high levels of both propionate and butyrate, an unusual SCFA combination. Hydrolytic degradation of CAX by acid hydrolysis (0.05 M oxalic acid at 100 °C for 2 h) and subsequent graded ethanol precipitations were used to obtain mixtures with different molecular weight ranges. Ethanol-precipitated fractions (F 0-65%, F 65-75%, F 75-85%) were mostly lower than 100 kDa and F > 85% was composed of monosaccharides and oligosaccharides of DP 2-8. Oxalic acid treatment caused the removal of all single arabinose unit branch chains and some di/trisaccharide branch chains, producing lightly substituted xylan backbone fragments, most of which were in the oligosaccharide (DP < 10) size range. In vitro human fecal fermentation analyses showed all oxalic acid-hydrolysate fractions were slower fermenting than fructooligosaccharides (FOS), but produced similar or higher amounts of total SCFAs. Butyrate production in two hydrolyzate fractions was double that of CH, while propionate levels remained relatively high.

Making the Case for Palliative Care at the System Level: Outcomes Data.

BACKGROUND: A recent trend in health care is to integrate palliative care (PC) programs across multiple hospitals to reduce variation, improve quality, and reduce cost. OBJECTIVE: The study objective was to demonstrate the benefits of PC for a system. METHODS: The study was a descriptive study using retrospective medical records in seven federated hospitals where PC developed differently before system integration. Measured were length of stay (LOS), mortality, readmissions, saved intensive care unit (ICU) days, cost avoidance, and hospice referrals. RESULTS: PC services within the first 48 hours of admission demonstrate a shorter LOS (5.08 days), reduced costs 40% ($2,362 per day), and decreased mortality (1.01 versus 1.10) for one hospital. Readmissions at 30, 60, and 90 days after a PC consult decreased (61.5%, 47.0%, and 42.1%, respectively). Annual pre- and postprogram referrals to hospice increased (65 to 107). Using modified matched pairs, LOS of PC patients seen within 48 hours of admission average 1.67 days less compared to non-PC patients. LOS for ICU patients with PC services in the ICU within the first 48 hours decreased by 1.12 days. Overall cost avoidance was 1.5 times total cost for PC programs systemwide. One pilot project using a full-time physician in the ICU reduced cost more than $600,000, with 315 saved ICU days, annualized. Systemwide, 69.3% of all referrals to hospice were made by the PC service. CONCLUSION: Early involvement of PC services emerged as advantageous to the net benefit. Given that health care's changing landscape will increasingly include bundled payment and risk holding strategies to improve quality and reduce cost in health care systems, systemwide PC will play a vital role.

Heat and pH stability of alkali-extractable corn arabinoxylan and its xylanase-hydrolyzate and their viscosity behavior.

UNLABELLED: In in vitro batch fermentations, both alkali-extractable corn arabinoxylan (CAX) and its xylanase-hydrolyzate (CH) were utilized by human fecal microbiota and produced similar short chain fatty acid (SCFA) contents and desirable long fermentation profiles with low initial gas production. Fortification of these arabinoxylans into processed foods would contribute desirable dietary fiber benefits to humans. Heat and pH stability, as well as viscosity behavior of CAX and CH were investigated. Size exclusion chromatography was used to analyze the molecular size distribution after treatment at different pH's and heating temperatures for different time periods. Treated under boiling and pressure cooking conditions at pH 3, CAX was degraded to a smaller molecular size, whereas the molecular size of the CH showed only a minor decrease. CAX and CH were mostly stable at neutral pH, except when CAX was treated under pressure for 60 min that slightly lowered molecular size. At 37 °C, neither CAX nor CH was adversely affected by treatment at low or neutral pH. The viscosities of solutions containing 5% and 10% of CAX were 48.7 and 637.0 mPa.s, respectively that were higher than those of solutions containing 5% and 10% of its hydrolyzate at shear rate 1 s⁻¹. The CAX solutions showed Newtonian flow behavior, whereas shear-thinning behavior was observed in CH solutions. In conclusion, the hydrolyzate of CAX has potential to be used in high fiber drinks due to its favorable fermentation properties, higher pH and heat stability, lower and shear-thinning viscosity, and lighter color than the native CAX. PRACTICAL APPLICATION: Arabinoxylan extracted by an alkali from corn bran is a soluble fiber with a desirable low initial and extended fermentation property. Corn arabinoxylan hydrolyzate using an endoxylanase was much more stable at different levels of acidity and heat than the native arabinoxylan, and showed lower solution viscosity and shear-thinning property that indicates its potential as an alternative functional dietary fiber for the beverage industry.

In vitro batch fecal fermentation comparison of gas and short-chain fatty acid production using "slowly fermentable" dietary fibers.

UNLABELLED: Sustained colonic fermentation supplies beneficial fermentative by-products to the distal colon, which is particularly prone to intestinal ailments. Blunted/delayed initial fermentation may also lead to less bloating. Previously, we reported that starch-entrapped alginate-based microspheres act as a slowly fermenting dietary fiber. This material was used in the present study to provide a benchmark to compare to other "slowly fermentable" fibers. Dietary fibers with previous reports of slow fermentation, namely, long-chain inulin, psyllium, alkali-soluble corn bran arabinoxylan, and long-chain ß-glucan, as well as starch-entrapped microspheres were subjected to in vitro upper gastrointestinal digestion and human fecal fermentation and measured over 48 h for pH, gas, and short-chain fatty acids (SCFA). The resistant fraction of cooked and cooled potato starch was used as another form of fermentable starch and fructooligosaccharides (FOS) served as a fast fermenting control. Corn bran arabinoxylan and long-chain ß-glucan initially appeared slower fermenting with comparatively low gas and SCFA production, but later fermented rapidly with little remaining in the final half of the fermentation period. Long-chain inulin and psyllium had slow and moderate, but incomplete, fermentation. The resistant fraction of cooked and cooled potato starch fermented rapidly and appeared similar to FOS. In conclusion, compared to the benchmark slowly fermentable starch-entrapped microspheres, a number of the purported slowly fermentable fibers fermented fairly rapidly overall and, of this group, only the starch-entrapped microspheres appreciably fermented in the second half of the fermentation period. PRACTICAL APPLICATION: Consumption of dietary fibers, particularly commercial prebiotics, leads to uncomfortable feelings of bloating and flatulence due to their rapid degradation in our large intestine. This article employs claimed potential slowly fermenting fibers and compares their fermentation rates with a benchmark slow fermenting fiber that we fabricated in an in vitro simulation of the human digestive system. Results show a variety of fermentation profiles only some of which have slow and extended rate of fermentation.

Validation of a motor activity system by a robotically controlled vehicle and using standard reference compounds.

INTRODUCTION: A series of experiments were undertaken to evaluate the accuracy, precision, specificity, and sensitivity of an automated, infrared photo beam-based open field motor activity system, the MotorMonitor v. 4.01, Hamilton-Kinder, LLC, for use in a good laboratory practices (GLP) Safety Pharmacology laboratory. METHODS: This evaluation consisted of two phases: (1) system validation, employing known inputs using the EM-100 Controller Photo Beam Validation System, a robotically controlled vehicle representing a rodent and (2) biologic validation, employing groups of rats treated with the standard pharmacologic agents diazepam or D-amphetamine. The MotorMonitor's parameters that described the open-field activity of a subject were: basic movements, total distance, fine movements, x/y horizontal ambulations, rearing, and total rest time. These measurements were evaluated over a number of zones within each enclosure. RESULTS: System validation with the EM-100 Controller Photo Beam Validation System showed that all the parameters accurately and precisely measured what they were intended to measure, with the exception of fine movements and x/y ambulations. Biologic validation using the central nervous system depressant diazepam at 1, 2, or 5 mg/kg, i.p. produced the expected dose-dependent reduction in rat motor activity. In contrast, the central nervous system stimulant D-amphetamine produced the expected increases in rat motor activity at 0.1 and 1 mg/kg, i.p, demonstrating the specificity and sensitivity of the system. DISCUSSION: Taken together, these studies of the accuracy, precision, specificity, and sensitivity show the importance of both system and biologic validation in the evaluation of an automated open field motor activity system for use in a GLP compliant laboratory.

Analysis of the logistic function model: derivation and applications specific to batch cultured microorganisms.

Mathematical models are useful for describing microbial growth, both in natural ecosystems and under research conditions. To this end, a rate expression that accounted for depletion of nutrients was used to derive the logistic function model for batch cultures. Statistical analysis was used to demonstrate the suitability of this model for growth curve data. Two linear forms of the model and two procedures for calculating growth rate constants were derived to facilitate statistical evaluation of growth curves. The procedures for calculating growth rate constants were found to be useful for calculation of growth rate constants at each time point, or for estimating growth rate constants from early growth curve data. The utility of the logistic function model and its alternative forms is discussed with respect to planning experiments, analyzing growth curves for the effects of factors other than nutrient limitation, and developing more complete descriptions of cell proliferation.