Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific... more
Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific value of this information to the understanding of biological systems requires computing and data storage technology of an unprecedented scale. The grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis. ...
We compared the abilities of Biolog’s GN and ECO plates to distinguish among aerobic and heterotrophic bacterial communities in samples from six aquatic environments. The Biolog system is based on interpreting patterns of sole-carbon... more
We compared the abilities of Biolog’s GN and ECO plates to distinguish among aerobic and heterotrophic bacterial communities in samples from six aquatic environments. The Biolog system is based on interpreting patterns of sole-carbon substrate utilization indicated by color development in a 96-well microtiter plate. Whether of fresh or saltwater origin, bacterial communities utilized >95% of substrates in both types of plates. Samples from any one environment exhibited similar time courses of average well color development (AWCD) in both GN and ECO plates. Principal component analysis was performed on data sets resulting from combinations of algorithms (AWCD and curve-integration methods) and levels of color development (end-point and set-point approaches). In all cases, the two types of plates demonstrated an equal capacity to discriminate among the heterotrophic expressions of the six microbial communities. Substantial deviation from an anticipated 1:1 correspondence occurred when color development of 25 substrates common to both types of plates was compared. The discrepancies likely are related to the different formulations of low-nutrient media in GN and ECO plates.
Synthetic biology is an emerging field that strives to build increasingly complex biological networks through the integration of molecular biology and engineering. The growth of the field has been supported by progress in the design and... more
Synthetic biology is an emerging field that strives to build increasingly complex biological networks through the integration of molecular biology and engineering. The growth of the field has been supported by progress in the design and construction of synthetic genetic and protein networks. This has led to the possibility of assembling modular components to attain novel biological functions and tools. In addition, these synthetic networks give rise to insights that facilitate the investigation of interactions and phenomena in naturally-occurring networks. Integration of well-characterized biological components into higher order networks requires computational modeling approaches to rationally construct systems that are directed towards a desired outcome. A computational approach would improve the predictability of the underlying mechanisms that would otherwise be difficult to deduce through experimentation alone. The analysis and interpretation of both qualitative and quantitative ...
Molecular and tissue damage induced by reactive oxygen species is a serious consequence of the production of free radicals in biological systems. Biological markers produced by reactions with hydroxyl radicals are useful indices of free... more
Molecular and tissue damage induced by reactive oxygen species is a serious consequence of the production of free radicals in biological systems. Biological markers produced by reactions with hydroxyl radicals are useful indices of free radical processesin vivo.In this respect, hydroxylation of aromatic compounds such as salicylate (2-hydroxybenzoate) has been used extensively as a measure of hydroxyl radical formation. 4-Hydroxybenzoate
a significant relationship was found between soluble P loss in runoff and soil test P. Eghball and Gilley (2001) Soils with high levels of P can contribute to excess P in runoff and found that erosion was the most important factor in... more
a significant relationship was found between soluble P loss in runoff and soil test P. Eghball and Gilley (2001) Soils with high levels of P can contribute to excess P in runoff and found that erosion was the most important factor in subsequently pollute the surface water. Excess P in the soil can be removed from the system by harvesting crops. The objectives of this loss of total and particulate P, whereas runoff amount, study were to evaluate corn (Zea mays L.) P removal effects on tillage, and P source were the important factors influencsoil P reduction, and to evaluate various corn hybrids and soybean ing loss of dissolved and bioavailable P in runoff. The [Glycine max (L.) Merr.] varieties for differences in grain P concentrasoil test P levels in this study did not seem to be high tion and P removal. Soil with varying P levels as a result of annual enough (ranged from 25 to 101 mg kg 1 in the top 5 cm or biennial beef cattle (Bos taurus) feedlot manure or compost applisoil) to ...
The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this... more
The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this process by modifying an existing or related model--suggesting nonlinear terms and structural modifications--or even constructing a new model that agrees with the system's time series
Ion channels play a crucial role in the physiology of complex biological systems because of their influence on the electrical equilibrium between the cells and their environment. From an engineering viewpoint, ion chan- nels will be the... more
Ion channels play a crucial role in the physiology of complex biological systems because of their influence on the electrical equilibrium between the cells and their environment. From an engineering viewpoint, ion chan- nels will be the key components of the design and the production of a new generation of biosensors integrat- ing the selectivity of ion channels with the
Several bacteriological surveys were performed from 1994 to 1996 at different Litopenaeus vannamei hatcheries (in Ecuador) and shrimp farms (in Mexico). Samples were taken from routine productions of healthy and diseased L. vannamei... more
Several bacteriological surveys were performed from 1994 to 1996 at different Litopenaeus vannamei hatcheries (in Ecuador) and shrimp farms (in Mexico). Samples were taken from routine productions of healthy and diseased L. vannamei larvae, postlarvae, and their culture environment and from healthy and diseased juveniles and broodstock. In Ecuador, the dominant bacterial flora associated with shrimp larvae showing symptoms of zoea 2 syndrome, mysis mold syndrome, and bolitas syndrome has been determined. Strains were characterized by Biolog metabolic fingerprinting and identified by comparison to a database of 850 Vibrio type and reference strains. A selection of strains was further genotypically fine typed by AFLP. Vibrio alginolyticus is predominantly present in all larval stages and is associated with healthy nauplius and zoea stages. AFLP genetic fingerprinting shows high genetic heterogeneity amongV. alginolyticus strains, and the results suggest that putative probiotic and pat...
I claim that explanations of human behaviour by Edward O. Wilsonand Charles Lumsden are constituted by a religiously functioningmetaphysics: emergent materialism. The constitutive effects areidentified using six criteria, beginning with a... more
I claim that explanations of human behaviour by Edward O. Wilsonand Charles Lumsden are constituted by a religiously functioningmetaphysics: emergent materialism. The constitutive effects areidentified using six criteria, beginning with a metaphorical re-description of dissimilarities between levels of organization interms of the lower level, and consist of conceptual andexplanatory reductions (CER). Wilson and Lumsden practice CER,even though CER is not
Biological processes and methods have been influencing science and technology for many decades. The ideas of feedback and control processes Norbert Wiener used in his cybernetics were based on observation of these phenomena in biological... more
Biological processes and methods have been influencing science and technology for many decades. The ideas of feedback and control processes Norbert Wiener used in his cybernetics were based on observation of these phenomena in biological systems. Artificial intelligence and intelligent systems have been fundamentally interested in the phenomenology of living systems, namely perception, decision-making, action, and learning. Natural systems exhibit many properties that form fundamentals for a number of nature inspired applications – dynamics, flexibility, robustness, self-organisation, simplicity of basic elements, and decentralization. This paper reviews examples of nature inspired software applications focused on optimization problems, mostly drawing inspiration from collective behaviour of social colonies.
Fatty acids play important roles in biological systems and the newborns fatty acids requirements are covered only by the milk. It is of particular interest to qualify the content of the fatty acids in the milk. This study was performed to... more
Fatty acids play important roles in biological systems and the newborns fatty acids requirements are covered only by the milk. It is of particular interest to qualify the content of the fatty acids in the milk. This study was performed to determine the levels of some fatty acids in the infant formulas and also to describe a method without derivatization for the fatty acids analysis and applying it to the control of infant formulas. Free fatty acids were produced by adding isopropanol- KOH to milk fat extract and heating it to saponify and acidify by H2SO4. Free fatty acids were extracted and were quantified by capillary gas chromatography on a fused silica column (AT-1000) and flame ionization detector. The average experimental values of lauric, palmitic, stearic and linoleic fatty acids contents of twenty infant formulas were 6.47, 16.52, 2.11 and 14.56 g/100g, respectively. The obtained experimental values of lauric and linoleic fatty acids contents of twenty infant formulas were ...
Abstract. Invariance is a necessary feature of a visual system able to recognize real objects in all their possible appearance. It is also the processing step most problematic to understand in biological systems, and most difficult to... more
Abstract. Invariance is a necessary feature of a visual system able to recognize real objects in all their possible appearance. It is also the processing step most problematic to understand in biological systems, and most difficult to simulate in computational models. This work investigates the possibility to achieve viewpoint invariance without adopting any explicit theorical solution to the problem, but simply by exposing a hierarchical architecture of self-organizing artificial cortical maps to series of images under various viewpoints. 1
Functionality of biological and inorganic systems ranging from nonvolatile computer memories and microelectromechanical systems to electromotor proteins and cellular membranes is ultimately based on the intricate coupling between... more
Functionality of biological and inorganic systems ranging from nonvolatile computer memories and microelectromechanical systems to electromotor proteins and cellular membranes is ultimately based on the intricate coupling between electrical and mechanical ...