Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme

In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.     

Simplified estimation technique for organic contaminant transport in groundwater

The analytical solution for one-dimensional dispersive—advective transport of a single solute in a saturated soil accompanied by adsorption onto soil surfaces and first-order reaction rate kinetics for degradation can be used to evaluate the suitability of potential sites for burial of organic chemicals. The technique can be used to the greatest advantage with organic chemicals that are present in groundwaters in small amounts. The steady-state solution provides a rapid method for chemical landfill site evaluation because it contains the important variables that describe interactions between hydrodynamics and chemical transformation. With this solution, solute concentration, at a specified distance from the landfill site, is a function of the initial concentration and two dimensionless groups. In the first group, the relative weights of advective and dispersive variables are compared, and in the second group the relative weights of hydrodynamic and degradation variables are compared. The ratio of hydr odynamic to degradation variables can be rearranged and written as (a_L·λ)/(q/ε), where a_L is the dispersivity of the soil, λ is the reaction rate constant, q is groundwater flow velocity, and ε is the soil porosity. When this term has a value less than 0.01, the degradation process is occurring at such a slow rate relative to the hydrodynamics that it can be neglected. Under these conditions the site is unsuitable because the chemicals are unreactive, and concentrations in groundwaters will change very slowly with distance away from the landfill site.     

Terrain simplification simplified: a general framework for view-dependent out-of-core visualization

We describe a general framework for out-of-core rendering and management of massive terrain surfaces. The two key components of this framework are: view-dependent refinement of the terrain mesh and a simple scheme for organizing the terrain data to improve coherence and reduce the number of paging events from external storage to main memory. Similar to several previously proposed methods for view-dependent refinement, we recursively subdivide a triangle mesh defined over regularly gridded data using longest-edge bisection. As part of this single, per-frame refinement pass, we perform triangle stripping, view frustum culling, and smooth blending of geometry using geomorphing. Meanwhile, our refinement framework supports a large class of error metrics, is highly competitive in terms of rendering performance, and is surprisingly simple to implement. Independent of our refinement algorithm, we also describe several data layout techniques for providing coherent access to the terrain data. By reordering the data in a manner that is more consistent with our recursive access pattern, we show that visualization of gigabyte-size data sets can be realized even on low-end, commodity PCs without the need for complicated and explicit data paging techniques. Rather, by virtue of dramatic improvements in multilevel cache coherence, we rely on the built-in paging mechanisms of the operating system to perform this task. The end result is a straightforward, simple-to-implement, pointerless indexing scheme that dramatically improves the data locality and paging performance over conventional matrix-based layouts.     

Identification of lead and other elements in ceramic glazes and housewares by 109Cd-induced X-ray fluorescence emission spectrometry

Hepatitis C virus (HCV) has been reported to conform to a quasispecies nature, which is most evident in hypervariable regions of the putative envelope 2 domain. The aim of this study was to determine the relationship between the nucleotide complexity and diversity of hypervariable region 1 and various stages of the carrier states. The subjects studied were 20 HCV carriers with normal alanine aminotransferase (ALT) levels, 50 patients with chronic hepatitis who showed elevated ALT levels, 22 with cirrhosis, and 24 with hepatocellular carcinoma. The quasispecies complexity was analyzed by means of polymerase chain reaction-mediated single strand conformation polymorphism (PCR-SSCP). The value of nucleotide diversity was calculated by PCR cloning and sequencing. The number of SSCP bands ranged from 1 to 7, with no significant differences in the mean numbers among the stages of HCV infection. There was no correlation between the amounts of serum HCV RNA and the numbers of SSCP bands. No significant difference was found in the values of nucleotide diversity between carriers with normal ALT levels (mean, 6.6 x 10(-2) per site) and patients with chronic hepatitis (7.7 x 10(-2). These findings suggest that the quasispecies complexity of hypervariable region 1 is independent of the stage of chronic HCV infection.     

Antibody to acetylcholine receptor in myasthenia gravis. Prevalence, clinical correlates, and diagnostic value

Elevated amounts of antibodies specific for acetylcholine receptors were detected in 87 percent of sera from 71 patients with myasthenia gravis but not in 175 sera from individuals without myasthenia gravis, including those with other neurologic or autoimmune diseases. Antireceptor antibodies were not directed at the acetylcholine binding site of the receptor. Presence or titer of antibody did not appear to correlate with age, sex, steroid therapy, or duration of symptoms. Myasthenia gravis patients with only ocular symptoms had lower antibody titers, while the majority of titers in myasthenia gravis patients with thymoma exceeded the median titer of the myasthenia gravis group as a whole. Assay of antireceptor antibody should prove a useful test in the diagnosis of myasthenia gravis.     

Substrate recruitment to cyclin-dependent kinase 2 by a multipurpose docking site on cyclin A

An important question in the cell cycle field is how cyclin-dependent kinases (cdks) target their substrates. We have studied the role of a conserved hydrophobic patch on the surface of cyclin A in substrate recognition by cyclin A-cdk2. This hydrophobic patch is approximately 35A away from the active site of cdk2 and contains the MRAIL sequence conserved among a number of mammalian cyclins. In the x-ray structure of cyclin A-cdk2-p27, this hydrophobic patch contacts the RNLFG sequence in p27 that is common to a number of substrates and inhibitors of mammalian cdks. We find that mutation of this hydrophobic patch on cyclin A eliminates binding to proteins containing RXL motifs without affecting binding to cdk2. This docking site is critical for cyclin A-cdk2 phosphorylation of substrates containing RXL motifs, but not for phosphorylation of histone H1. Impaired substrate binding by the cyclin is the cause of the defect in RXL substrate phosphorylation, because phosphorylation can be rescued by restoring a cyclin A-substrate interaction in a heterologous manner. In addition, the conserved hydrophobic patch is important for cyclin A function in cells, contributing to cyclin A's ability to drive cells out of the G1 phase of the cell cycle. Thus, we define a mechanism by which cyclins can recruit substrates to cdks, and our results support the notion that a high local concentration of substrate provided by a protein-protein interaction distant from the active site is critical for phosphorylation by cdks.     

The Recording of Echocardiograms with an Intensity-Modulated Ink-Jet Oscillograph

Echocardiography is today well established and has gained widespread acceptance as a clinical routine method, especially for the diagnosis of mitral valve stenosis. Since heart structure movements are relatively fast, only information of limited medical value can be obtained from direct inspection of the A-scope display. Ideally, an apparatus for recording the movements of heart structures in the form of curves should record multiple reflected echoes and should also be able to record simultaneously other heart parameters such as ECG, phonocardiogram, or blood pressure.     

Local vibrational modes of the oxygen-vacancy complex in germanium

Infrared absorption of n-and p-Ge crystals enriched with ¹⁶O and/or ¹⁸O isotopes was studied after irradiation with 6-MeV electrons. Absorption spectra were measured at 10 and 300 K. Along with known bands characteristic of oxygen-containing defects, new lines at 669, 944, and 990 cm^?1 were detected. These bands are annealed at temperatures of 120–140°C; the band at 621 cm^?1, previously related to the vacancy-oxygen complex in Ge, is simultaneously annealed. The bands at 621 and 669 cm^?1 showed identical temperatures (10 → 300 K) and oxygen isotope (¹⁶O → ¹⁸O) shifts. These bands were found to correspond to various charge states of a defect with an energy level near E_v=0.25±0.03 eV. It is assumed that such a defect is the vacancy-oxygen complex (A center). The weak bands at 944 and 990 cm^?1 were identified as combinations of asymmetric stretching modes at 621 and 669 cm^?1 with a symmetric one at 320 cm^?1 for neutral and negative charge states of the A center, respectively.     

Streaming simplification of tetrahedral meshes

Unstructured tetrahedral meshes are commonly used in scientific computing to represent scalar, vector, and tensor fields in three dimensions. Visualization of these meshes can be difficult to perform interactively due to their size and complexity. By reducing the size of the data, we can accomplish real-time visualization necessary for scientific analysis. We propose a two-step approach for streaming simplification of large tetrahedral meshes. Our algorithm arranges the data on disk in a streaming, I/O-efficient format that allows coherent access to the tetrahedral cells. A quadric-based simplification is sequentially performed on small portions of the mesh in-core. Our output is a coherent streaming mesh which facilitates future processing. Our technique is fast, produces high quality approximations, and operates out-of-core to process meshes too large for main memory     

Optimal cut-off for obesity and markers of metabolic syndrome for Ethiopian adults

Background

Metabolic syndrome (MetS) is defined as the presence of central obesity plus any two of the following markers: high triglycerides (>?150 mg/dl), low high density lipoprotein (HDL) cholesterol <?40 mg/dl in men and?<?50 mg/dl in women, hypertension (blood pressure?>?130/85 mmHg or use of antihypertensive medication), high fasting blood glucose (>?100 mg/dl or use of treatment for diabetes mellitus). Since recently, metabolic syndrome and obesity have become emerging problems of both low and middle income countries, although they have been the leading cause of morbidity and mortality in high income countries for the past decades. It has been indicated that the international anthropometric cut-off for detecting obesity is not appropriate for Ethiopians. This study developed optimal cut off values for anthropometric indicators of obesity and markers of metabolic syndrome for Ethiopian adults to enhance preventive interventions.

Methods

A total of 704 employees of Jimma University were randomly selected using their payroll as a sampling frame. Data on socio-demographic, anthropometry, clinical and blood samples were collected from February to April 2015. Receiver Operating Characteristic Curve analyses were used to determine optimal anthropometric cut-off values for obesity and markers of the metabolic syndrome. WHO indicators of obesity based on body fat percent (>?25% for males and?>?35% for females) were used as binary classifiers for developing anthropometric cut-offs. Optimal cut-off values were presented using sensitivity, specificity and area under the curve.

Results

The optimal cut-off for obesity using body mass index was 22.2 k/m² for males and 24.5 kg/m² for females. Similarly, the optimal waist circumference cut-off for obesity was 83.7 cm for males and 78.0 cm for females. The cut-off values for detecting obesity using waist to hip ratio and waist to height ratio were: WHR (0.88) and WHtR (0.49) for males, while they were 0.82 and 0.50 for females, respectively. Anthropometric cut-off values for markers of metabolic syndrome were lower compared to the international values. For females, the optimal BMI cut-offs for metabolic syndrome markers ranged from 24.8 kg/m² (triglycerides) to 26.8 kg/m² (fasting blood sugar). For WC the optimal cut-off ranged from of 82.1 cm (triglyceride) to 96.0 cm(HDL); while for WHtR the optimal values varied from 0.47(HDL) to 0.56(fasting blood sugar). Likewise, the optimal cut-offs of WHR for markers of metabolic syndrome ranged from 0.78(fasting blood sugar) to 0.89(HDL and blood pressure). For males, the optimal BMI cut-offs for metabolic syndrome markers ranged from 21.0 kg/m² (HDL) to 23.5 kg/m² (blood pressure). For WC, the optimal cut-off ranged from 85.3 cm (triglyceride) to 96.0 cm(fasting blood sugar); while for WHtR the optimal values varied from 0.47(BP, FBS and HDL) to 0.53(Triglyceride). Similarly, the optimal cut-offs of WHR form markers of metabolic syndrome ranged from 0.86(blood pressure) to 0.95(fasting blood sugar).

Conclusion

The optimal anthropometric cut-offs for obesity and markers of metabolic syndrome in Ethiopian adults are lower than the international values. The findings imply that the international cut-off for WC, WHtR, WHR and BMI underestimate obesity and metabolic syndrome markers among Ethiopian adults, which should be considered in developing intervention strategies. It is recommended to use the new cut-offs for public health interventions to curb the increasing magnitude of obesity and associated metabolic syndrome and diet related non-communicable diseases in Ethiopia.