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Without magic bullets: the biological basis for public health interventions against protein folding disorders Nature Precedings
Rodrick Wallace.
Protein folding disorders of aging like Alzheimer's and Parkinson's diseases currently present intractable medical challenges. 'Small molecule' interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary 'physics' or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty's (2010a) elegant exploration of the genetic code. The formalism produces...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4847/version/1
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Ablation of smooth muscle myosin heavy chain SM2 increases smooth muscle contractility and results in postnatal death in mice Nature Precedings
Mei Chi; Yingbi Zhou; Srikanth Vedamoorthyrao; Gopal Babu; Muthu Periasamy.
The smooth muscle myosin heavy chains (SMHC) are motor proteins powering smooth muscle contraction. Alternate splicing of SHMC gene at the C-terminus produces SM1, and SM2 myosin isoforms; SM2 (200 kDa) contains a unique 9-amino-acid sequence at the carboxyl terminus, whereas SM1 (204 kDa) has a 43 amino acid non-helical tail region. To date the functional difference between C-terminal isoforms has not been established; therefore, we used an exon-specific gene targeting strategy and generated a mouse model specifically deficient in SM2. Deletion of exon-41 of the SMHC gene resulted in a complete loss of SM2 in homozygous (_SM2^-/-^_) mice, accompanied by a concomitant down-regulation of SM1 in bladders. While heterozygous (_SM2^+/-^_) mice appeared normal...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1643/version/1
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Activation of Ras-ERK pathway by Fgf8 and its downregulation by Sprouty2 for the isthmus organizing activity Nature Precedings
Asuka Suzuki-Hirano; Tatsuya Sato; Harukazu Nakamura.
In the previous studies, we showed that strong Fgf8 signaling activates the Ras-ERK pathway to induce cerebellum. Here, we show importance of negative regulation of this pathway. 'Prolonged' activation of ERK by misexpression of _Fgf8b_ and dominant-negative _Sprouty2_ (_dnSprouty2_) did not change the fate of the mesencephalic alar plate. Downregulation of ERK activity using a MEK inhibitor, U0126, or by tetracycline dependent Tet-off system after co-expression of _Fgf8b_ and _dnSprouty2_, forced the mesencephalic alar plate to differentiate into cerebellum. We then paid attention to Mkp3. After misexpression of _dnMkp3_ and _Fgf8b_, slight downregulation of ERK activity occurred, which may be due to Sprouty2, and the mesencephalon...
Tipo: Manuscript Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2089/version/1
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Regulation of Phosphatase Homologue of Tensin Protein Expression by Bone Morphogenetic Proteins in Prostate Epithelial Cells Nature Precedings
Travis Jerde; Zhong Wu; Dan Theodorescu; Wade Bushman.
Phosphatase homologue of tensin (PTEN) is the key endogenous inhibitor of phosphoinositide signaling and is the most commonly mutated gene in human prostate cancer. The bone morphogenetic proteins (BMPs) are secreted developmental signaling molecules known to promote differentiation in the prostate. BMP ligands have been shown to inhibit prostate cancer cell line proliferation and tumor growth and expression of BMPs, BMP ligands, receptors and signaling effectors are diminished in prostate cancer. A previous report in the colon led us to investigate the potential mechanistic relationship between PTEN and BMP signaling in prostate epithelial cells. We show here that BPM signaling positively regulates PTEN in normal and malignant prostate cells by increasing...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4311/version/1
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Numbers, not value, motivate cooperation in humans and orangutans Nature Precedings
Ellen E. Furlong; John E. Opfer.
Cooperation among competitors-whether sharing the burden of wind resistance in the Tour de France, forming price-fixing cartels in economic markets, or adhering to arms-control agreements in international treaties-seldom spreads in proportion to the potential benefits. To gain insight into the minds of uncooperative agents, economists and social psychologists have used the prisoner's dilemma task to examine factors leading to cooperation among competitors. Two types of factors have emerged in these studies: the relative rewards of defecting versus cooperating and breakdowns in trust, forgiveness and communication. The generalizability of economic and social psychological factors, however, relies on the assumption that agents' comparisons...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology.
Ano: 2007 URL: http://precedings.nature.com/documents/1392/version/1
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3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone Nature Precedings
Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone. Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol. To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone. These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol. Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR]. Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5. Mutant...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6216/version/1
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Diet transition to a high-fat diet for 3 weeks reduces brain omega-3-fatty acid levels, alters BDNF signaling and induces anxiety & depression-like behavior in adult rats Nature Precedings
Sandeep Sharma; Yumei Zhuang; Fernando Gomez-Pinilla.
Background: The consumption of diets high in calories and low in nutrient value is becoming increasingly common in modern society, which can lead to metabolic disorders like diabetes and obesity, and potentially to psychiatric disorders. We have performed studies to assess how the shift from a healthy diet rich in omega-3 fatty acids to a diet rich in saturated fatty acid affects the substrates for brain plasticity and function, and anxiety and depression-like behavior. Methods: Pregnant rats were fed with omega-3 supplemented diet from their 2nd day of gestation period as well as their male pups for 12 weeks. Afterwards, the animals were randomly assigned to either a group fed on the same diet or a group fed on a high-fat diet (HFD) rich in saturated fats...
Tipo: Manuscript Palavras-chave: Developmental Biology; Neuroscience; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6950/version/1
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Enhancing Jatropha Productivity by Canopy Management Nature Precedings
Chalapathy K. Reddy; Vishal V. Naole.
Jatropha seed and oil yield is function of planting material used, growing conditions, plant architecture development and maintenance. Jatropha is hardy plant; thrives well in arid and semi arid regions with an average rainfall ranging from 500 to 1200 mm. It has been planted in varied soil types, marginal and waste lands; where in utilization of in situ resources by agronomic practices and development and management of canopy by pruning are very crucial for harvesting higher seed for biodiesel production. Building ideal canopy by pruning during first growing season is very important. Pruning is done during winter season when plants are in dormant condition.
Tipo: Manuscript Palavras-chave: Developmental Biology; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3700/version/1
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Porous Chitsan-Gelatin Scaffolds Embedded with PLGA Nanoparticles for Bone Repair Nature Precedings
Vijay Kumar Nandagiri; Piergiergio Gentile; Valeria Chiono; Clara Muttu; Gianluca Ciardelli; Franco Maria Montevecchi; Ziebun Ramtoola.
Bone regeneration can be accelerated by localized delivery of appropriate growth factors/bio active molecules. Localized delivery can be achieved by incorporating bioactive molecules within biodegradable particulate carrier system followed by embed them in a suitable porous scaffolds. These carrier system facilitates the impregnated growth factor(s) to release at a desirable rate and concentration, and to linger at injury sites for a sufficient time to recruit progenitors and stimulate tissue healing processes. In this study, an attempt has been made to engraft the porous chitosan-gelatin scaffolds with PLGA nanoparticles for localized delivery of bioactive components. Scaffolds loaded with PLGA nanoparticles were subjected to physical and mechanical...
Tipo: Poster Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4728/version/1
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Analysis of Endocrine Disruption in Southern California Coastal Fish using an Aquatic Multi-Species Microarray Nature Precedings
Michael E. Baker; Barbara Ruggeri; James Sprague; Colleen Eckhardt; Jennifer Lapira; Ivan Wick; Laura Soverchia; Massimo Ubaldi; Alberta M. Polzonetti-Magni; Doris Vidal-Dorsch; Steven Bay; Joseph R. Gully; Jesus A. Reyes; Kevin M. Kelley; Daniel Schlenk; Ellen C. Breen; Roman Šášik; Gary Hardiman.
BACKGROUND: Endocrine disruptors include plasticizers, pesticides, detergents and pharmaceuticals. Turbot and other flatfish are used to characterize the presence of chemicals in the marine environment. Unfortunately, there are relatively few genes of turbot and other flatfish in GenBank, which limits the use of molecular tools such as microarrays and qRT-PCR to study disruption of endocrine responses in sentinel fish captured by regulatory agencies.
OBJECTIVES: A multi-gene cross species microarray was fabricated as a diagnostic tool to screen the effects of environmental chemicals in fish, for which there is minimal genomic information. The array included genes that are involved in the actions of adrenal and sex steroids, thyroid...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2823/version/1
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Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements. (Version 2.0) Nature Precedings
Valentin Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional “wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6231/version/2
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Production of Transgenic Cloned Miniature Pigs with Membrane-bound Human Fas Ligand (FasL) by Somatic Cell Nuclear Transfer Nature Precedings
Jae Goo Seol; Soo Hyun Kim; Dong-Il Jin; Seung Pyo Hong; Ji Yeon Yoo; Ki Myung Choi; Young Chul Park; Yun Jin Yun; Kwang Wook Park; Jae Young Heo.
Cell-mediated xenograft rejection, including NK cells and CD8+ CTL, is a major obstacle in successful pig-to-human xenotransplantation. Human CD8+ CTL and NK cells display high cytotoxicity for pig cells, mediated at least in part by the Fas/FasL pathway. To prevent cell-mediated xenocytotoxicity, a membrane-bound form of human FasL (mFasL) was generated as an inhibitor for CTL and NK cell cytotoxicity that could not be cleaved by metalloproteinase to produce putative soluble FasL. We produced two healthy transgenic pigs harboring the mFasL gene via somatic cell nuclear transfer (SCNT). In a cytotoxicity assay using transgenic clonal cell lines and transgenic pig ear cells, the rate of CD8+ CTL-mediated cytotoxicity was significantly reduced in transgenic...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Immunology.
Ano: 2010 URL: http://precedings.nature.com/documents/4539/version/1
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Soybean Composition Database from NIR, NMR and GC-MS Analyses Nature Precedings
I. C. Baianu.
This novel Soybean Composition Database from the AFC-NMR & NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.
Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. 

A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6201/version/1
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Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth Nature Precedings
I. C. Baianu.
Experimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7128/version/1
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Weight Stigma and Educators' Perceptions of Children's Psychological Symptoms Nature Precedings
John Pryor; Laura Reber.
Objective: To investigate whether weight stigma influences educators' judgments about psychological symptoms in children.Design: Experimental study manipulating the weight status of children with school problems and examining implicit and explicit anti-fat attitudes as potential moderators of stigmatizing judgments.Subjects: 188 pre-service educators.Measurements: Attributions of laziness as primary dependent variable plus measures of implicit and explicit anti-fat attitudes as potential moderators.Results: Educators were more likely to attribute laziness to overweight children with school problems. Implicit anti-fat attitudes moderated this effect.Conclusion: Spontaneous anti-fat attitudes were importantly related to educators' biases in...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2133/version/1
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Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness Nature Precedings
Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5059/version/1
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Complex Systems Biology of Organisms Nature Precedings
I. C. Baianu.
Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine's logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7044/version/1
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Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (OBESINDEX) generated by the association between body fat and body mass index Nature Precedings
Joao L. M. C. Azevedo; Susana A. Miyahira; Lucas P. F. F. Leal; Glicia C. Azevedo; Otavio C. Azevedo; Joao L. C. Azevedo; Gustavo P. S. Miguel.
Background: A Fuzzy Obesity Index (OBESINDEX) for use as an alternative in bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for...
Tipo: Manuscript Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5516/version/1
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Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species Nature Precedings
I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7083/version/2
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The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification Nature Precedings
Gizachew Tiruneh.
*Objective*: To investigate the best statistical models that describe the effect of physical activity on BMI.
*Design*: Cross-sectional analyses of physical activity and BMI data. 
*Subjects*: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m2, respectively).
*Measurements*: Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/2758/version/5
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