BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Background  

Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use.     

Effect of pepsin on partially purified pig gastric mucus and purified mucin

Partially purified native-pig gastric mucus and purified pig gastric mucin, prepared by column chromatography and caesium chloride (CsCl) density-gradient ultracentrifugation, were subjected to pepsin digestion. The products of peptic digestion were chromatographed on Sepharose CL-2B, and fractions were assayed for carbohydrate by the periodic acid-Schiff reaction. The polymeric gastric mucin in the purified mucin samples was readily degraded by pepsin. In sharp contrast, the polymeric mucin in the partially purified mucus was relatively resistant to pepsin digestion. In 45 min, pepsin degraded 40% of the polymeric mucin in the purified samples, whereas it produced no significant degradation (less than 10%) in the partially purified mucus samples. In partially purified gastric mucus, treated with CsCl but not fractionated by ultracentrifugation, digestion with pepsin was also slow and incomplete. This showed that differences in susceptibility between partially purified and purified preparations are not due to the chaotropic effects of CsCl. In addition, the recombination of low-density nonmucin fractions in CsCl ultracentrifugation with the mucin also resisted pepsin digestion. Finally, we have shown that the low-density fractions in mucus exhibited a strong inhibitory effect of peptic activity in vitro. We conclude that under our experimental conditions, pepsin has little effect on partially purified mucus, and our findings indicate an inhibitor of peptic digestion is present in native gastric mucus. It is likely, but unproven, that this inhibitor is a noncovalently bound lipid present in the low-density fraction.     

Cranial postnatal growth of the rat relative to environmental variance

Neurocranial growth during the first 40 days of postnatal development was biometrically investigated relative to the specific parameters of calvarium length and width; basioccipital length and width; basisphenoid length; biparietal width; frontal bone length and cranial vault length. Specimens were obtained from rat litters subject to moderate nutritional suppression by raising the litter numbers above the norm via the cross-fostering technique and causing the overtaxing of the lactational capacity. Alterations in growth rate occurred throughout the pre- and postweaning periods with clearly demarcated phases of growth. Male and female growth in the preweaning period was uniform within each litter type but the phasic growth changes in the experimental litters differed from the control litters with regression line breakage emerging at different points and altering the phasic lengths. The preweaning phasic spectrum in both control and experimental litters was evidently linked to the maternal lactation capacity--relative to quantity and duration. Weaning was insidious in both litter types but occurred earlier in the experimental litters although the continuity of growth was maintained up to the end of the definitive preweaning period (day 20). The definitive postweaning period (day 21-40) showed considerable heterogeneity--unsatisfactory scatter--with differing regression line breakage points and phasic lengths. Analysis based on the total period (day 1-40) brought compensatory adjustments and indicated more acceptable phasic patterns in the postweaning period with confirmation of catch-up growth in the experimental litters. Allometric analysis of the parameters revealed varying rates of growth, line breakage points and differing phasic lengths indicating that each neurocranial parameter and the skeletal unit forming it had an individual characteristic response spectrum mostly attributable to the functional matrix with emphasis on the capsular rather than the periosteal.     

Topotaxis: A New Mechanism of Directed Cell Migration in Topographic ECM Gradients

Living cells orient the cytoskeleton polarity and directional migration in response to spatial gradients of multiple types of cues. The resulting tactic behaviors are critical for the proper cell localization in the context of complex single-cell and tissue behaviors. In this perspective, we highlight the recent discovery of, to our knowledge, a new -taxis phenomenon, the topotaxis, which mediates directional cell migration in response to the gradients of such topographic features as the density of extracellular matrix fibers. The direction of topotactic migration critically depends on the effective stiffness of the cortical cytoskeleton, which is controlled by the balance between two parallel signaling pathways activated by the extracellular matrix input. Topotaxis can account for such striking cell behaviors as the opposite directionality of migration of benign and metastatic cancer cells and certain aspects of the wound-healing process. We anticipate that, in conjunction with other tactic phenomena, topotaxis can provide critical information for understanding and design of tissue structure and function.     

Variation in the growth of the preweaning Syrian hamster (Cricetus auratus)

An assessment of the growth rate spectrum based on a longitudinal weight study of golden hamsters was undertaken over the preweaning period. The period covered 23 days with data probes at 24-hourly intervals and encompassed 16 litters providing a birth number of 120 young and a weaning survival number of 82. Subsequent analysis directed initially at the pooled or averaged data showed sex differences with males gaining weight faster than females. Further analysis showed the total period to have three definitive break-points and therefore four phases of growth activity. The segmented linear regression line calculations showed that the phasic duration of males in the second and third phases were two days later than the females. Following data-analysis adjustments and taken into account aberrations of the sample, final indications pointed to the preweaning hamster growth spectrum as quadrophasic, exhibiting a stable first phase, a second and third phase terminating earlier in females and a final weaning weight being heavier in males. The growth curves demonstrated a 'U' shaped outline and formed an integral part of hamster preweaning precocity.