simulation of biological processes in the genome context

... concern the process of developing scienti¢c software The codes involved in simulation software are becoming larger and larger In engineering, they range from 50 000 lines to perhaps 000 000 lines of ... In that Empire, the art of cartography attained such perfection that the map of a single province occupied the entirety of a city, and the map of the Empire, the entirety of a province In ... on-line tools for data mining, homology searching, sequence alignment and numerous other analyses One of the best entry points for those interested in the burgeoning ¢eld of bioinformatics is the...

Ngày tải lên: 11/04/2014, 09:47

... part  of the lost  wave  energy  is  transformed  into  turbulence  energy.  At  the beginning  of the wave  breaking  process,  the turbulence  is  confined into a small portion of the breaking  ... wetted function is 1. For other cases, value of the cell  side  wetted  function  equals  to  the ratio of the length of the wetted portion over  the total length of the cell side. After getting  all the wetted points on four sides of the cell,  ... by  the dotted line in Fig. 1. The wetted area in cell i,j  in this  figure  is  the portion  of the cell  from  the dotted  line  to  offshore.  The wetted  periphery  and  area  inside ...

Ngày tải lên: 28/03/2014, 15:20

... abundant in the genomes of bacterial pathogens As expected, the authors confirmed that The Importance of Biological Interactions in the Study of Biodiversity the presence of these prophages was in ... selection in an environment such as a biofilm leads to the evolution of unequal interactions Specific mutations in the genome of one species lead to adaptation to the presence of the other The resulting ... detected in any section of the crypt region Biofilms are the leading cause of contamination of medical devices and in industrial and agricultural settings The initial adhesion and further colonization...

Ngày tải lên: 28/06/2014, 08:20

... on-line tools for data mining, homology searching, sequence alignment and numerous other analyses One of the best entry points for those interested in the burgeoning ¢eld of bioinformatics is the ... So, the questions to be debated at this meeting will include: What does in silico refer to and include? What are the roles of modelling in biology? What is the role of mathematics in modelling? ... set the scene for one of the debates that will feature again in this meeting, which is the issue of reduction versus integration There cannot be any doubt that most of the major successes in biological...

Ngày tải lên: 06/08/2014, 13:22

... concern the process of developing scienti¢c software The codes involved in simulation software are becoming larger and larger In engineering, they range from 50 000 lines to perhaps 000 000 lines of ... In that Empire, the art of cartography attained such perfection that the map of a single province occupied the entirety of a city, and the map of the Empire, the entirety of a province In ... of the machines in the TOP500 list of the leading 500 supercomputers in the world which are prepared to provide details of their systems The SGI machines tend to be used for scienti¢c computing,...

Ngày tải lên: 06/08/2014, 13:22

... wrong in the strict sense of the word, how we know that we are justi¢ed in using the model in a particular context? In going from the gene to the whole organism, biological systems consist of an interaction ... models have proved to be an invaluable tool for the understanding of the essential mechanisms underlying the patterning processes in the BZ reaction in the way that the study of a detailed computational ... a minimal model, both from the point of view of the mathematical insight that it provides, and also from the practical point of view of being able to use a reduced form of a model as a building...

Ngày tải lên: 06/08/2014, 13:22

... found in the genome, in this case in the E coli genome The connection pattern of coloured boxes then indicates the presence of the bacteria-type lysine biosynthesis pathway Thus, given the reference ... clear about the functions of the database regarding the purpose of modelling According to the decision we have made at this stage of de¢ning the purpose of the database, there is a series of speci¢cations ... developing bioinformatics technologies for deciphering the genome in terms of the biological system at the cellular level; namely, in terms of systemic functional behaviours of the cell or the single-celled...

Ngày tải lên: 06/08/2014, 13:22

... experimental investigations o¡er the promise of providing data pertaining to the above steps A major challenge, then, is the organization of this data into knowledge in the form of hypothesis, models ... pathways Thus, if the digital signature of protein kinase A in two di¡erent pathways is the same, then the kinase is in the same functional state in the two pathways Middle tier The middle tier ... another selection to ¢nd the interacting partner The protein and its interacting partners will be displayed as nodes on the GUI Each node can now act as a further starting point, and the interaction...

Ngày tải lên: 06/08/2014, 13:22

... to the template in order to map points in this template to points in the target The bottom panel shows the result of applying the inverse mapping f to the target to take this target back into the ... surprising change in the apparent ¢bre orientation in the septum in the failing dog hearts Could this be due to something other than a change in the principal axis of the myocytes, and instead ... shows the result of applying the forward mapping f to the template (C), and the inverse mapping fÀ1 to the target (D); the right column shows the grids deformed by the forward mapping f (E) and the...

Ngày tải lên: 06/08/2014, 13:22

... eleven binary £ags Ten of these represent the state of binding or modi¢cation sites: aspartate binding (1); CheBp binding (2); CheR binding (3); methylation (4^7); phosphorylation (8); CheY binding ... residues on the cytoplasmic domain of MCPs Each added methyl group increases the activity of CheA in complex with the receptor, thereby counteracting the e¡ect of attractant binding Methylesterase/deamidase ... ignores the downstream phosphorylation cascade The full complement of receptor states should include, in addition, the binding of ligand in the periplasm and of the modi¢cation enzymes, as well as the...

Ngày tải lên: 06/08/2014, 13:22

... working in simulation studies in engineering or cosmology or in many other physical sciences And, in fact, the failure of the MNT model is one of the most instructive examples of experiment ^simulation ... point of view, they are also in uencing the younger scientists We shouldn’t be giving up on them From the point of view of the science of biology, there are many of these scientists and they are ... is the fate of insights that were hard-won at the time to become obvious later This review will also therefore serve the purpose of reminding readers of the role simulation played in gaining them...

Ngày tải lên: 06/08/2014, 13:22

... proteins often regulate their own production or that of other proteins in a complex web of interactions The biochemistry of the feedback loops in protein^DNA interactions often leads to non-linear ... the beginning of this meeting, which is that what you call something does actually matter Presumably, it will matter from the point of view of the way in which you organize the database of information ... can bring together many di¡erent forms of data, all of which are directly applicable to the particular experiment being performed The data are constrained from the beginning of the modelling process...

Ngày tải lên: 06/08/2014, 13:22

... described in the text, plus control This IKr model was then included into a model of the action potential (B) The simulated action potentials for the same four cases as in Panel A The e¡ect of cAMP independent ... for handling the current state of biological knowledge: there is a wide variation in the amount of available data Motif-based modelling allows the investigator to use a combination of heuristic ... great deal of data Collecting these data is a very labour intensive process There is the possibility that constructing models of the action of this drug for the 160 that you want to eliminate can...

Ngày tải lên: 06/08/2014, 13:22

... transgenic rice genome The results of PCRs would confirm the appearance of the AtAOS2 gene in the transgenic rice genome MATERIALS AND METHODS 2.1 Extraction of rice DNA The leaves of one-month-old ... Dr.Eunsun Kim) In this study, a set of PCRs was carried out to detect the hygromycin resistance gene, CaMV35S promoter (the promoter located in front of the AtAOS2 gene), and the AtAOS2 gene in the transgenic ... thaliana AOS2 gene in the rice genome CONCLUSION From the above results, the hygromycin resistance gene, CaMV35S promoter (the promoter located in front of the AtAOS2 gene), and the AtAOS2 gene...

Ngày tải lên: 06/08/2014, 18:21

... B.Sc in civil engineering in 1969 from the Catholic University of Louvain, his M.Sc in civil and geological engineering in 1970 from Princeton University, and his Ph.D in environmental engineering ... establishment of the Australian Institute of Marine Science more than 25 years ago This book contains important chapters dealing with different aspects of the functioning of the ecosystem in relation to the ... negate the claims of another, so that the media and the decision-makers are left in doubt as to the security of the information they are receiving Yet we have a more secure information base than the...

Ngày tải lên: 12/08/2014, 05:21

... demonstrate the relevance of science and the need for science in planning the future of the GBR The book emphasises multi-disciplinary processes, i.e., physics–biology links, as these emerge as the dominant ... alone Reinforcing the findings of McCook et al., Fabricius and De’ath (Chapter 9, this book) quantify the influence of turbidity in determining spatial patterns of soft coral biodiversity on the ... they can glue onto them and entrain them downward to their death The water circulation over the mud shoals fringing the mangroves encourages the recruitment of prawn larvae spawned offshore The...

Ngày tải lên: 12/08/2014, 05:21

... references therein) More recently, the role of the grazing industry has received attention as a sediment source since grazing is the dominant land use upstream of the coastal floodplains of many of Queensland’s ... to the GBRMP In contrast to the bigger basins, in particular the Fitzroy and the Burdekin, substantial conversion of woody vegetation to more intensive agricultural use is taking place in the interior ... mm dϪ1 The samples were collected either by lowering a bucket from a bridge at a point above the centre of the flowing part of the channel, or more directly by wading into the stream The samples...

Ngày tải lên: 12/08/2014, 05:21

... European cropping and pastoral activities in the catchments adjoining the GBR CATCHMENTS ADJOINING THE GBR Continental drainage basins with an aggregate area of 425,000 km drain into the Great Barrier ... entering at the upper end In contrast, the integrated flux of DON at Ingham is circa 87% of the nominal input flux Particulate N fluxes at the downstream site are approximately 1.8 times the input ... area of the GBR catchment is or was covered by woodlands or savanna woodlands Open range cattle grazing is the principal land use in these areas The most complete record of gauged runoff into the...

Ngày tải lên: 12/08/2014, 05:21

... nutrient against light limitation of seagrass growth, the light condition bringing about the elevated amino acid content in the plants 13 In response to shading and increased water depth, the carbon ... Ecosystems of the World 24, Intertidal and Littoral Ecosystems Elsevier, Amsterdam, 572 pp Brown, B.E & Holley, M.C 1981 The influence of tin smelting and tin dredging on the intertidal reef flats of ... (discharge) for the peak rainfall month RESPONSES OF MANGROVES TO SILTATION Siltation is of primary importance in the development of mangroves In deltas along the coasts of Southeast Asia, mangroves...

Ngày tải lên: 12/08/2014, 05:21

... implications in terms of attributing causality of the decline in coral cover The immediate cause of the coral death may be natural, but the failure to recover, and consequent long-term decline in reef ... the moving indicator on the graph The changes between algal and coral dominance are portrayed by the varying proportion of the two scenes at the bottom Initial conditions were set to be low in ... across the shelf The effect of the flood plumes are simulated by brief “nutrient pulses” of decreasing strength to the north of the mouth of the Herbert River, simultaneous with disturbances The...

Ngày tải lên: 12/08/2014, 05:21