Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier

A computational model is presented for the simulation of three-dimensional electrodiffusion of ions. Finite volume techniques were used to solve the Poisson-Nernst-Planck equation, and a dual Delaunay-Voronoi mesh was constructed to evaluate fluxes of ions, as well as resulting electric potentials. The algorithm has been validated and applied to a generalized node of Ranvier, where numerical results for computed action potentials agree well with cable model predictions for large clusters of voltage-gated ion channels. At smaller channel clusters, however, the three-dimensional electrodiffusion predictions diverge from the cable model predictions and show a broadening of the action potential, indicating a significant effect due to each channel's own local electric field. The node of Ranvier complex is an elaborate organization of membrane-bound aqueous compartments, and the model presented here represents what we believe is a significant first step in simulating electrophysiological events with combined realistic structural and physiological data.     

Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms

Background

Multiple protein templates are commonly used in manual protein structure prediction. However, few automated algorithms of selecting and combining multiple templates are available.

Results

Here we develop an effective multi-template combination algorithm for protein comparative modeling. The algorithm selects templates according to the similarity significance of the alignments between template and target proteins. It combines the whole template-target alignments whose similarity significance score is close to that of the top template-target alignment within a threshold, whereas it only takes alignment fragments from a less similar template-target alignment that align with a sizable uncovered region of the target. We compare the algorithm with the traditional method of using a single top template on the 45 comparative modeling targets (i.e. easy template-based modeling targets) used in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7). The multi-template combination algorithm improves the GDT-TS scores of predicted models by 6.8% on average. The statistical analysis shows that the improvement is significant (p-value < 10^-4). Compared with the ideal approach that always uses the best template, the multi-template approach yields only slightly better performance. During the CASP7 experiment, the preliminary implementation of the multi-template combination algorithm (FOLDpro) was ranked second among 67 servers in the category of high-accuracy structure prediction in terms of GDT-TS measure.

Conclusion

We have developed a novel multi-template algorithm to improve protein comparative modeling.     

Substrate usage during prolonged exercise following a preexercise meal

The effect of a high-carbohydrate meal 4 h before 105 min of exercise at 70% of maximal O2 uptake was determined in seven endurance-trained cyclists and compared with exercise following a 16-h fast. The preexercise meal produced a transient elevation of plasma insulin and blood glucose, which returned to fasting basal levels prior to the initiation of exercise. The meal also resulted in a 42% elevation (P less than 0.05) of glycogen within the vastus lateralis at the beginning of exercise. The 1st h of exercise when subjects were fed was characterized by a 13-25% decline (P less than 0.05) in blood glucose concentration, a suppression of the normal increase in plasma free fatty acids and blood glycerol, and a 45% (P less than 0.05) greater rate of carbohydrate oxidation compared with exercise when subjects were fasted. After 105 min of exercise, there were no significant differences when subjects were fed or fasted regarding blood glucose levels, rate of carbohydrate oxidation, or muscle glycogen concentration. The greater muscle glycogen utilization (97 +/- 18 vs. 64 +/- 8 mmol glucosyl units X kg-1; P less than 0.05) and carbohydrate oxidation when subjects were fed appeared to be derived from the glycogen synthesized following the meal. These results indicate that preexercise feedings alter substrate availability despite a return of plasma insulin to fasting levels prior to exercise and that these effects persist until the 2nd h of exercise.     

Horizontal transmission, vertical inactivation, and stochastic loss of mariner-like transposable elements

Horizontal transmission has been well documented as a major mechanism for the dissemination of mariner-like elements (MLEs) among species. Less well understood are mechanisms that limit vertical transmission of MLEs resulting in the "spotty" or discontinuous distribution observed in closely related species. In this article we present evidence that the genome of the common ancestor of the melanogaster species subgroup of Drosophila contained an MLE related to the mellifera (honey bee) subfamily. Horizontal transmission, approximately 3-10 MYA, is strongly suggested by the observation that the sequence of the MLE in Drosophila erecta is 97% identical in nucleotide sequence with that of an MLE in the cat flea, Ctenocephalides felis. The D. erecta MLE has a spotty distribution among species in the melanogaster subgroup. The element has a high copy number in D. erecta and D. orena, a moderate copy number in D. teissieri and D. yakuba, and was apparently lost ("stochastic loss") in the lineage leading to D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. In D. erecta, most copies are concentrated in the heterochromatin. Two copies from D. erecta, denoted De12 and De19, were cloned and sequenced, and they appear to be nonfunctional ("vertical inactivation"). It therefore appears that the predominant mode of MLE evolution is vertical inactivation and stochastic loss balanced against occasional reinvasion of lineages by horizontal transmission.      

Budding yeast morphogenesis: signalling, cytoskeleton and cell cycle

Yeast-like fungi such as Saccharomyces cerevisiae exhibit a range of cell types differing in cell shape, gene expression and growth pattern. Signal transduction pathways mediate transitions between different cell types. Nutritional signals induce rounded yeast-form cells either to enter invasive growth as elongated filamentous cells or to arrest to prepare for stationary phase, conjugation, or meiosis. An emerging theme is that development critically depends upon differential regulation of vegetative functions, including cytoskeletal organization and cell cycle progression, as much as on the expression of cell type specific gene products.     

Exercise metabolism at different time intervals after a meal

To determine how long a meal will affect the metabolic response to exercise, nine endurance-trained and nine untrained subjects cycled for 30 min at 70% of peak O2 consumption (VO2 peak) 2, 4, 6, 8, and 12 h after eating 2 g carbohydrate/kg body wt. In addition, each subject completed 30 min of cycling 4 h after the meal at an intensity that elicited a respiratory exchange ratio (RER) of 0.94-0.95. During exercise after 2 and 4 h of fasting, carbohydrate oxidation was elevated 13-15% compared with the response to exercise after an 8- and 12-h fast (P less than 0.01). The increase in blood glycerol concentration during exercise (30 to 0 min) was linearly related to the length of fasting (r = 0.99; P less than 0.01). In all subjects, plasma glucose concentration declined 17-21% during exercise after 2 h of fasting (P less than 0.01). Plasma glucose concentration also declined (15-25%) during exercise in the trained subjects after 4 and 6 h of fasting (P less than 0.05) but did not change in the untrained subjects. However, the decline in plasma glucose concentration was similar (14%) in the two groups when the exercise intensity was increased in the trained subjects (i.e., 78 +/- 1% VO2 peak) and decreased in the untrained subjects (i.e., 65 +/- 3% VO2 peak) to elicit a similar RER.(ABSTRACT TRUNCATED AT 250 WORDS)     

Warthin''s tumour: unusual vs. common morphological findings in fine needle aspiration biopsies

Fine needle aspiration biopsies (FNA) of 47 Warthin's tumours confirmed by histology were re-evaluated for cytomorphological findings. The majority of aspirates (37/47) contained a typical background with proteinaceous substance and cell debris, along with cellular elements represented by oncocytic, lymphoid, and mast cells with degranulated cytoplasm. Uncommon cellular findings were true squamous cells (1/47), atypical cells with vacuoles (1/47), osteoclastic giant cells (1/47), epithelioid cells (1/47), mast cells with preserved granules in cytoplasm (3/47), and siderophages (4/47). Uncommon findings in the background were corpora amylacea-like structures and homogeneous bright red droplets. Squamous cells and atypical cells with vacuoles caused diagnostic difficulties in distinguishing a Warthin's tumour from a squamous cell or mucoepidermoid carcinoma. However, other unusual cellular and background findings were not worrying; therefore, they are merely regarded as a curiosity in the cytomorphological appearance of the tumour.     

Water in the Avian Egg Overall Budget of Incubation

The loss of mass in eggs during incubation was examined andevidence is presented to show that this is essentially due toloss of water. The mean fraction of water lost by diffusionthroughout incubation is 0.150 ± 0.025 S D per gram ofegg and 0.162 ± 0.026 S D per gram of egg content for81 species. The water fraction of fresh eggs and of hatchingeggs was examined in 32 species divided according to maturityat hatching, and found to be very similar within each category(83% in altricial 83% in semi-altricial 78% in semi-precocial72% in precocial eggs). The 11% difference between the altricialand precocial categories is statistically significant. Duringincubation, dry matter is metabolized increasing the water fractionwhich is further increased by metabolic water production. Hence,water loss during incubation is mandatory if the relative watercontent of an egg at the end of incubation is to remain essentiallythe same as at the beginning. Equations are developed whichallow one to estimate the difference between diffusive waterloss and the total water loss in altricial and piecocial eggscaused by additional water loss during pipping and hatching.     

Gas Exchange of the Avian Egg Time, Structure, and Function

Data are presented for oxygen consumption water loss duringincubation water vapor conductance of the shell and pore numberof avian eggs and the way in which these values relate not onlyto egg mass but also to incubation time. It is proposed thatall these functions are proportional to the product of egg massand rate of development where the latter is defined as the inverseof incubation time. These interrelationships account at theend of incubation for similar O₂ and CO₂ tensions in the airspace of eggs utilization of calories (0.5 kcal g^–1) andwater loss (15 g g^–1)     

Aspects of the biology of Nezumia aequalis from the continental slope west of the British Isles

Nezumia aequalis is one of the most abundant fishes on the upper and middle continental slopes (500–1750 m depth zones) of the North-east Atlantic with a peak abundance of three to four individuals 1000 m⁻² swept area in the 750-m zone. Mean and modal size increased with depth, fish from the Rockall Trough (RT) being larger than those at equivalent depths in the Porcupine Seabight (PSB). Sex ratios were close to parity in all depth zones. Females grew larger than males. Head length to total length and to total weight did not differ significantly between sexes but RT fish were heavier at any given length than PSB fish. Serial batch spawning occurred over the first three quarters of the year. Ovaries contained five size groups of eggs, the three largest groups being vitelline and contributing 27% of the absolute individual fecundity which was positively correlated with body size and ranged from 9109 to 26 847. Age determined from sagittal otoliths ranged from 1 to 10 years, the ageing method being validated by a time-series study of the growing edge of otoliths. The von Bertalanffy growth parameter ( k ) was estimated at 0·175 and 0·216 from head length and otolith length, respectively.