http://precedings.nature.com/subjects/development/ Recently posted documents in Developmental Biology Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3894/version/2 We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of human biology into the center of biological psychiatry. The cultural and epigenetic systems of heritage may well provide the ‘missing’ heritability of complex diseases now under so much intense discussion. http://precedings.nature.com/documents/3894/version/2 Wed, 11 Nov 2009 18:29:58 UTC The cultural epigenetics of psychopathology: The missing heritability of complex diseases found? hdl:10101/npre.2009.3894.2 2009-11-11 Rodrick Wallace Nature Precedings 2009-11-11T18:29:58Z Manuscript Developmental Biology Genetics & Genomics Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3913.1 A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests. http://dx.doi.org/10.1038/npre.2009.3913.1 Thu, 29 Oct 2009 10:09:24 UTC Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico doi:10.1038/npre.2009.3913.1 2009-10-29 Nature Precedings 2009-10-29T10:09:24Z Manuscript Biotechnology Developmental Biology Genetics & Genomics Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3873/version/1 The underlying cellular and molecular mechanisms that regulate and coordinate critical physiological processes such as peristalsis are complex, often cryptic, and involve the integration of multiple tissues and organ systems within the organism. We have identified a completely novel component of the larval autonomic nervous system in the Drosophila larval midgut that is essential for the peristaltic movement of food from the anterior midgut into the acidic region of the midgut. We have named this region the Superior Cupric Autonomic Nervous System or SCANS. Located at the junction of the anterior and the acidic portions of the midgut, the SCANS is characterized by a cluster of a novel neuro-enteroendocrine cells that we call Lettuce Head Cells, a valve, and two anterior muscular tethers to the dorsal gastric caeca. Using cell ablation and ectopic activation via expression of the Chlamydomonas reinhardtii blue-light activated channelrhodopsin, we demonstrate that the SCANS and in particular the Lettuce Head Cells are both necessary and sufficient for peristalsis and perhaps serve a larger role by coordinating digestion throughout the anterior midgut with development and growth. http://precedings.nature.com/documents/3873/version/1 Fri, 23 Oct 2009 18:56:19 UTC Regulated peristalsis into the acidic region of the Drosophila larval midgut is controlled by a novel component of the Autonomic Nervous System hdl:10101/npre.2009.3873.1 2009-10-23 Dennis Richard LaJeunesse Nature Precedings 2009-10-23T18:56:19Z Manuscript Developmental Biology Neuroscience http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3894/version/1 We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of human biology into the center of biological psychiatry. The cultural and epigenetic systems of heritage may well provide the ‘missing’ heritability of complex diseases now under so much intense discussion. http://precedings.nature.com/documents/3894/version/1 Fri, 23 Oct 2009 11:39:41 UTC The cultural epigenetics of psychopathology: The missing heritability of complex diseases found? hdl:10101/npre.2009.3894.1 2009-10-23 Rodrick Wallace Nature Precedings 2009-10-23T11:39:41Z Manuscript Developmental Biology Genetics & Genomics Neuroscience http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3845/version/1 Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally. http://precedings.nature.com/documents/3845/version/1 Fri, 09 Oct 2009 09:45:29 UTC A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation hdl:10101/npre.2009.3845.1 2009-10-09 Satya N. V. Arjunan Nature Precedings 2009-10-09T09:45:29Z Manuscript Developmental Biology Microbiology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3832.1 Background: The assumption of an invariant fat-free or lipid-free composition is prerequisite for most methods of the estimation of body composition in mammals including human but has not been theoretically demonstrated.Objective: To demonstrate theoretically and practically the invariant lipid-free composition and to understand the mechanism varying the main components of muscle and adipose tissue which have intimate relationships to lipid accumulation or obesity in mammals. Design: Whether the combinations of correlations among energy and main components in the hypothetical lipid-ratio variation model (L-varied model), which reflects the invariant lipid-free composition, are consistent with those in the practical mammal meats? Do lipid-ratio variation (L-varied) equations based on L-varied model agree closely with the corresponding regression equations of energy and main components on lipid content in their meats? We designed to solve these questions and compare those results. Results: These combinations of their correlations between the theoretical model and practical meats stated above were consistent with each other. And the L-varied equations were consistent with the regression equations stated above. Conclusion: It is clarified that variation in energy reserves and main components, at least moisture, protein, and ash in them follow L-varied model. Consequently, for the first time we clearly demonstrated here that the assumption of an invariant lipid-free composition is valid in skeletal muscles and peripheral adipose tissues of some mammals. http://dx.doi.org/10.1038/npre.2009.3832.1 Wed, 07 Oct 2009 13:50:05 UTC The demonstration of the invariant lipid-free composition and the mechanism varying energy and the main components of some mammal meats consisting of muscle and adipose tissue doi:10.1038/npre.2009.3832.1 2009-10-07 Mitsugu Inoue Nature Precedings 2009-10-07T13:50:05Z Manuscript Developmental Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3828/version/1 Limusaurus is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II & III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, & IV in other amniotes. Limusaurus has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, & IV, thus explaining the embryological position of bird wing digits. However, morphology and gene expression of the anterior bird wing digit specifically resemble digit I, not II, of other amniotes. We argue that digit I loss in Limusaurus is derived and thus irrelevant to understanding the development of the bird wing. http://precedings.nature.com/documents/3828/version/1 Tue, 06 Oct 2009 12:15:57 UTC Limusaurus and bird digit identity hdl:10101/npre.2009.3828.1 2009-10-06 Alexander O. Vargas Nature Precedings 2009-10-06T12:15:57Z Manuscript Developmental Biology Genetics & Genomics Molecular Cell Biology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3809.1 Plant cell cultures of Taxus provide the most reliable production methods for the anti-cancer drug paclitaxel. In order to comprehend the inherent culture heterogeneity and production variability in cell cultures, it is essential that the cellular metabolism is studied at the genomic level. Genomic stability in plant cell cultures is crucial as it affects cell growth and division, metabolite accumulation and protein synthesis. A rapid and efficient method to prepare nuclei suspensions from aggregated cell cultures of Taxus was employed. Methods were subsequently developed to simultaneously stain them for DNA and protein content using Propidium Iodide and Fluorescein Isothiocyanate respectively. Flow cytometry was used to analyze and quantify the DNA content and genome size of Taxus using known reference species as standards. Furthermore, their genomic stability was evaluated by correlating DNA content and genome size with cell size and complexity, protein content, and elicitation effects using multiparameter flow cytometry. These techniques to evaluate and correlate various culture characteristics can be very useful in designing superior bio processes for enhanced production. http://dx.doi.org/10.1038/npre.2009.3809.1 Thu, 01 Oct 2009 08:33:37 UTC Nuclear DNA and protein content evaluation in Taxus plant cell cultures using multiparameter flow cytometry doi:10.1038/npre.2009.3809.1 2009-10-01 Vishal Gaurav Nature Precedings 2009-10-01T08:33:37Z Poster Biotechnology Cancer Developmental Biology Genetics & Genomics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3787/version/1 Objective: To determine iron bioavailability in obese subjects after the ingestion of a nutritional supplement containing multiple nutrients. Methods: Fourteen persons were studied before and after bariatric surgery after the ingestion of a nutritional formulation containing 25 mg iron, 25 g fiber and 800 mg calcium. Serum iron levels were measured basally and every hour after the ingestion of 200 mL of the formulation, and serum ferritin, unsaturated iron binding capacity (UIBC), hemoglobin, albumin, total proteins, total triglycerides, total cholesterol and fractions (LDL-cholesterol and HDL-cholesterol) sere determined at the same time points.Results: The following ferremia values (median/minimum – maximum) were obtained before and after bariatric surgery, respectively: Fasting, 105 (70 – 364) µg/dL and 198 (38 – 617) µg/dL; 1 hour, 103 (63 – 305) µg/dL and 160 (11 – 207) µg/dL; 2 hours, 103 (62 – 150) µg/dL and 141 (10 – 412) µg/dL; 3 hours. 97 (63 – 190) µg/dL and 153 (6 – 270) µg/dL; 4 hours, 91 (58 – 163) µg/dL and 156 (40 – 251) µg/dL (p>0.05), with no association of serum iron levels with time. There was a difference in total triglycerides (95 ± 29 mg/dL and 60 ± 10 mg/dL) which were correlated with a decrease in serum ferritin levels (r = 0,926, p = 0.008), UIBC (r = 0.910, p = 0.01), total cholesterol (r = 0,918, p = 0.01) and LDL-c fraction (r = 0.830, p = 0.04), with an increase in HDL-c fraction (r = 0,807, p = 0.05). Conclusion: Iron bioavailability in obese subjects was affected by the ingestion of the nutritional formulation containing calcium and fiber and the serum ferritin and UIBC values involved in the body metabolism of iron were reduced by the surgery, a fact that may cause these patients to develop iron deficiency. http://precedings.nature.com/documents/3787/version/1 Mon, 21 Sep 2009 14:50:35 UTC Iron (FeSO4) Bioavailability in Obese Subjects Submitted to Bariatric Surgery hdl:10101/npre.2009.3787.1 2009-09-21 Luciana Bueno Nature Precedings 2009-09-21T14:50:35Z Manuscript Biotechnology Chemistry Developmental Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3697/version/1 Crystallized intelligence (Gc) is thought to reflect skills acquired through knowledge and experience and is related to verbal ability, language development1 and academic success2. Gc, together with fluid intelligence (Gf), are constructs of general intelligence3. While Gc involves learning, knowledge and skills, Gf refers to our ability in tests of problem-solving, pattern matching, and reasoning. Although there is evidence that Gf can be improved through memory training in adults4, the efficacy of memory training in improving acquired skills, such as Gc and academic attainment, has yet to be established. Furthermore, evidence of transfer effects from gains made in the trained tasks is sparse5. Here we demonstrate improvements in Gc and academic attainment using working memory training. Participants in the Training group displayed superior performance in all measures of cognitive assessments post-training compared to the Control group, who received knowledge-based training. While previous studies have indicated that gains in intelligence are due to improvements in test-taking skills6, this study demonstrates that it is possible to improve crystallized skills through working memory training. Considering the fundamental importance of Gc in acquiring and using knowledge and its predictive power for a large variety of intellectual tasks, these findings may be highly relevant to improving educational outcomes in those who are struggling. http://precedings.nature.com/documents/3697/version/1 Wed, 02 Sep 2009 08:38:39 UTC The efficacy of working memory training in improving crystallized intelligence hdl:10101/npre.2009.3697.1 2009-09-10 Tracy Alloway Nature Precedings 2009-09-02T08:38:39Z Manuscript Developmental Biology http://creativecommons.org/licenses/by/3.0/