A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Impact of Diet and Quality Grade on Shelf Life of Beef Steaks

Steers were fed a diet containing dry rolled corn, steam flaked corn, dry rolled corn with 30% dried distillers grains, or steam flaked corn with 30% dried distillers grains. Strip loins from upper 2/3 Choice and Select- grade carcasses were obtained to evaluate the effects of diet and quality grade on shelf life characteristics. Strip loins were aged for 2, 9, 16, or 23 days. Results suggest that steaks from cattle fed steam flaked corn (with or without dried distillers grains) and from cattle fed dried distillers grains (regardless of corn type) had higher levels of many unsaturated fatty acids, more discoloration, and greater lipid oxidation compared to the dry rolled corn treatments or the no dried distillers grains treatments, respectively. Feeding of dry rolled corn or diets without dried distillers grains maintained red color better during retail display. Choice- grade steaks had significantly higher levels of unsaturated fatty acids like 18:2 and total polyunsaturated fatty acids than Select- grade steaks but did not diff er in color stability or oxidation. These data indicate the longest shelf life will occur when cattle are fed diets containing dry rolled corn (versus steam flaked corn) or without dried distillers grains (versus with dried distillers grains) and that both steam flaked corn and distillers grains have a negative impact on shelf life. Quality grade did not affect color stability

Energy Landscapes of Perfect and Defective Solids:from Structure Prediction to Ion Conduction

Abstract The energy landscape concept is increasingly valuable in understanding and unifying the structural, thermodynamic and dynamic properties of inorganic solids. We present a range of examples which include (i) structure prediction of new bulk phases including carbon nitrides, phosphorus carbides, LiMgF 3 and low-density, ultra-flexible polymorphs of B 2 O 3, (ii) prediction of graphene and related forms of ZnO, ZnS and other compounds which crystallise in the bulk with the wurtzite structure, (iii) solid solutions, (iv) understanding grossly non-stoichiometric oxides including the superionic phases of δ-Bi 2 O 3 and BIMEVOX and the consequences for the mechanisms of ion transport in these fast ion conductors. In general, examination of the energy landscapes of disordered materials highlights the importance of local structural environments, rather than sole consideration of the average structure

Modelling proteins’ hidden conformations to predict antibiotic resistance

AbstractTEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM’s specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models’ prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.</jats:p

Quality Effects on Beef from Cattle Fed High-Protein Corn Distillers Grains and Other Ethanol By-Products

The objective of this study was to evaluate the effects of feeding high protein corn distillers grains on fresh beef quality. Steers were fed one of five diets, either a corn control, high protein distillers grains plus solubles, dry distillers grains plus solubles, wet distillers grains plus solubles, or bran plus solubles diet. Strip loins were aged for 2, 9, or 23 days and placed under retail display conditions for 0 or 7 days. Dietary treatment had no effect on tenderness within each aging period. There were also no differences between treatments for proximate composition, free calcium in the muscle, and sarcomere length. Results suggest that feeding high protein distillers grains decreases color stability and increases lipid oxidation when compared to corn diets leading to reduced shelf life

Impact of Myoglobin Oxygenation State on Color Stability of Frozen Beef Steaks

The objective of this study was to determine the impacts of myoglobin oxygenation level and frozen storage duration on frozen beef color. Strip loins were wet- aged for 4 or 20 days and were fabricated into steaks that were assigned a myoglobin oxygenation level (highly oxygenated, lowly oxygenated, or deoxymyoglobin) and packaging film (impermeable or permeable). Steaks were then frozen for 0, 2, 4, or 6 months of storage and analyzed for various beef color measurements. Highly oxygenated steaks had greater a* values (redness) and percent oxymyoglobin compared to the other treatments. Frozen storage beyond 4 months and oxygen impermeable packaging tended to have detrimental effects on beef color. Highly oxygenated steaks that are aged for 4 d displayed superior red color for extended storage with few undesirable effects

The Relationship of Liver Abscess Scores and Early Postmortem Meat Tenderness

Acidosis is one of the most common nutritional disorders found in commercial feedlots. Cattle diets with high concentrations of starch can cause rapid production of acids in the rumen, disrupting microbial fermentation, causing liver abscess formation, and lowering livestock performance. This study was conducted to evaluate the relationship between the occurrence of liver abscesses and beef tenderness early postmortem. Results showed numerically lesser shear force values (greater tenderness) in loins from animals without liver abscesses, however, this was not statistically significant for slice shear force or Warner- Bratzler shear force. Although the effects of liver abscess occurrence in relation to meat quality are still unclear, results from this study provide a conceptual foundation for additional research to be explored on meat quality

Proteomic Analysis of Oxidized Proteins in Beef

To evaluate the effects of diet and quality grade on tenderness and oxidative damage to proteins, strip loins from USDA Upper 2/3rd Choice and Select- grade carcasses were obtained. Steers were fed either a diet containing dry rolled corn, steam flaked corn, dry rolled corn with 30% dried distillers grains with solubles, or steam flaked corn with 30% dried distillers grain with solubles. Results suggest that steaks from steers fed dry rolled corn are more objectively tender than steam flaked corn; in addition, steaks grading USDA Upper 2/3rd Choice steaks were more tender when compared to USDA Select quality grade. In contrast to previous research, no tenderness differences were detected between steaks from steers with or without dried distillers with solubles. Proteomic analysis revealed increased oxidative damage of myofibrillar proteins. Steaks graded as USDA Upper 2/3rd Choice steaks were determined to generally have increased oxidative damage to glycolytic, structural, and heat shock proteins, compared to USDA Select quality grade. While samples from steers fed dry rolled corn were more tender and had increased myofibrillar oxidative damage from steers fed DRC with distillers grains, steam flaked corn- related treatment displayed the inverse response. Overall, results support the relationship between marbling and tenderness, and suggest oxidative stress may be a factor involved in this difference

Impact of Diet and Quality Grade on Shelf Life of Beef Steaks

Steers were fed a diet containing dry rolled corn, steam flaked corn, dry rolled corn with 30% dried distillers grains, or steam flaked corn with 30% dried distillers grains. Strip loins from upper 2/3 Choice and Select- grade carcasses were obtained to evaluate the effects of diet and quality grade on shelf life characteristics. Strip loins were aged for 2, 9, 16, or 23 days. Results suggest that steaks from cattle fed steam flaked corn (with or without dried distillers grains) and from cattle fed dried distillers grains (regardless of corn type) had higher levels of many unsaturated fatty acids, more discoloration, and greater lipid oxidation compared to the dry rolled corn treatments or the no dried distillers grains treatments, respectively. Feeding of dry rolled corn or diets without dried distillers grains maintained red color better during retail display. Choice- grade steaks had significantly higher levels of unsaturated fatty acids like 18:2 and total polyunsaturated fatty acids than Select- grade steaks but did not diff er in color stability or oxidation. These data indicate the longest shelf life will occur when cattle are fed diets containing dry rolled corn (versus steam flaked corn) or without dried distillers grains (versus with dried distillers grains) and that both steam flaked corn and distillers grains have a negative impact on shelf life. Quality grade did not affect color stability

Galaxy Zoo: star formation versus spiral arm number

Spiral arms are common features in low-redshift disc galaxies, and are prominent sites of star formation and dust obscuration. However, spiral structure can take many forms: from galaxies displaying two strong ‘grand design’ arms to those with many ‘flocculent’ arms. We investigate how these different arm types are related to a galaxy's star formation and gas properties by making use of visual spiral arm number measurements from Galaxy Zoo 2. We combine ultraviolet and mid-infrared (MIR) photometry from GALEX and WISE to measure the rates and relative fractions of obscured and unobscured star formation in a sample of low-redshift SDSS spirals. Total star formation rate has little dependence on spiral arm multiplicity, but two-armed spirals convert their gas to stars more efficiently. We find significant differences in the fraction of obscured star formation: an additional ∼10 per cent of star formation in two-armed galaxies is identified via MIR dust emission, compared to that in many-armed galaxies. The latter are also significantly offset below the IRX–β relation for low-redshift star-forming galaxies. We present several explanations for these differences versus arm number: variations in the spatial distribution, sizes or clearing time-scales of star-forming regions (i.e. molecular clouds), or contrasting recent star formation histories