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Experimental Technologies (experimental + technology)
Selected AbstractsGenome-scale models of bacterial metabolism: reconstruction and applicationsFEMS MICROBIOLOGY REVIEWS, Issue 1 2009Maxime Durot Abstract Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities. [source] Bayesian analysis of single-molecule experimental dataJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 3 2005S. C. Kou Summary., Recent advances in experimental technologies allow scientists to follow biochemical processes on a single-molecule basis, which provides much richer information about chemical dynamics than traditional ensemble-averaged experiments but also raises many new statistical challenges. The paper provides the first likelihood-based statistical analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single deoxyribonucleic acid (DNA) hairpin molecule. The conformational change is initially treated as a continuous time two-state Markov chain, which is not observable and must be inferred from changes in photon emissions. This model is further complicated by unobserved molecular Brownian diffusions. Beyond the simple two-state model, a competing model that models the energy barrier between the two states of the DNA hairpin as an Ornstein,Uhlenbeck process has been suggested in the literature. We first derive the likelihood function of the simple two-state model and then generalize the method to handle complications such as unobserved molecular diffusions and the fluctuating energy barrier. The data augmentation technique and Markov chain Monte Carlo methods are developed to sample from the posterior distribution desired. The Bayes factor calculation and posterior estimates of relevant parameters indicate that the fluctuating barrier model fits the data better than the simple two-state model. [source] Desert water harvesting from takyr surfaces: assessing the potential of traditional and experimental technologies in the KarakumLAND DEGRADATION AND DEVELOPMENT, Issue 1 2007L. Fleskens Abstract From historical times the traditionally nomadic people in desert environments of Turkmenistan have applied a range of innovative technologies to secure water supply for consumptive and productive purposes. These technologies make use of takyrs, flat or slightly sloping dense clay surfaces which act as natural catchment areas. In recent history, these technologies have been neglected, in part due to a booming water supply through irrigation development, and takyr surfaces have suffered various degradation processes. However, the limited scope for further extension of irrigation systems presents a challenge to reconsider these traditional technologies. In this paper, results of cost-benefit analysis are presented by which an assessment is made of the potential of both traditional and experimental takyr use technologies. It is shown that they bear considerable potential for the future at relatively low investment cost, that they may help limit degradation processes and provide for a sustainable development pathway for the inhabitants of the desert. A main challenge in order to benefit from this potential is to find an appropriate management structure for maintenance and resource use of these water-harvesting technologies. Copyright © 2006 John Wiley & Sons, Ltd. [source] Brain edema in liver failure: Basic physiologic principles and managementLIVER TRANSPLANTATION, Issue 11 2002Fin Stolze Larsen MD In patients with severe liver failure, brain edema is a frequent and serious complication that may result in high intracranial pressure and brain damage. This short article focuses on basic physiologic principles that determine water flux across the blood-brain barrier. Using the Starling equation, it is evident that both the osmotic and hydrostatic pressure gradients are imbalanced across the blood-brain barrier in patients with acute liver failure. This combination will tend to favor cerebral capillary water influx to the brain. In contrast, the disequilibration of the Starling forces seems to be less pronounced in patients with cirrhosis because the regulation of cerebral blood flow is preserved and the arterial ammonia concentration is lower compared with that of patients with acute liver failure. Treatments that are known to reverse high intracranial pressure tend to decrease the osmotic pressure gradients across the blood-brain barrier. Recent studies indicate that interventions that restrict cerebral blood flow, such as hyperventilation, hypothermia, and indomethacin, are also efficient in preventing edema and high intracranial pressure, probably by decreasing the transcapillary hydrostatic pressure gradient. In our opinion, it is important to recall that rational fluid therapy, adequate ventilation, and temperature control are of direct importance to controlling cerebral capillary water flux in patients with acute liver failure. These simple interventions should be secured before more advanced experimental technologies are instituted to treat these patients. [source] Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomicsNEW PHYTOLOGIST, Issue 3 2008Xinyou Yin Summary Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem. [source] | ||||||||||