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11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2 Nature Precedings
Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4649/version/1
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3D model of amphioxus steroid receptor complexed with estradiol Nature Precedings
Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR....
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3316/version/1
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3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol Nature Precedings
Michael E. Baker; David J. Chang; Charlie Chandsawangbhuwana.
Lamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor. A perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids. For example, 15[alpha]-hydroxy-estradiol [15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2). To investigate how 15[alpha]-OH-E2 binds lamprey ER, we constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2. Our 3D model shows that S[delta] on Met-409 can form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2. In human ER[alpha], the corresponding residue Ile-424 has a van der Waals contact with 15[alpha]-OH-E2. BLAST analysis of GenBank indicates that among vertebrate ERs, only lamprey ER contains a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2768/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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A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers Nature Precedings
Fucheng Zhang; Zhonghe Zhou; Xing Xu; Xiaolin Wang; Corwin Sullivan.
Recent coelurosaurian discoveries have greatly enriched our knowledge of the dinosaur-bird transition, but all reported taxa close to this transition are from relatively well-known coelurosaurian groups^1-3^. Here we report a new basal avialan, Epidexipteryx hui gen. et sp. nov., from the Middle-Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis shows it to be the sister taxon to Epidendrosaurus^4,5^, forming a new clade at the base of Avialae^6^. Epidexipteryx also possesses two pairs of elongate ribbon-like tail feathers (ETFs), and its limbs lack contour feathers for flight. This finding...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2326/version/1
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A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics Nature Precedings
I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7052/version/1
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A Hypothetic Mechanism of Ordering and Shaping Cells within Discrete Regions Nature Precedings
Yaroslav Strokovskyy.
We propose a hypothetic mechanism of ordering and shaping cells during _C. elegans_ embryogenesis. The mechanism is based on the assumption that during each round of division of cells, daughter cells acquire electric charges from its mother cells (charge conservation law is taken into account). Between the acts of division, the total electric field, generated by a system of charged cells, change relative positions of the charged cells within the region. In one’s turn, the positions of the charged cells determine the pattern of the electrostatic field. A mathematical model of such self-consistent mechanism is developed. The process of developing the sixteen-cell structure starting with one cell is simulated. The results correspond to the known...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4277/version/1
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A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation Nature Precedings
Satya N. V. Arjunan; Masaru Tomita.
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...
Tipo: Manuscript Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3845/version/1
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A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements- (v.4) 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/4
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A Rate Distortion approach to protein symmetry Nature Precedings
Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein 'molten globule'. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript Palavras-chave: Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4280/version/1
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A Study of prevalence of malnutrition in government School children in the field area of Azad nagar Bangalore, India Nature Precedings
Izhar Hasan.
Malnutrition is a problem at varying proportions in developing countries, and anthropometry is a simple tool to assess its magnitude in children. This study was aimed at identifying the prevalence of malnutrition among 500 children of govt schols of Azad Nagar, bangalore south Asia. The value of using various field based formulae and of various anthropometric indicators used for classification of malnutrition was also studied. The study was focused on children aged 8-14 years studying in class 1st to 8th in govt schools. Anthropometric data and eating practices of children were collected with the help of a pretested questionnaire and food intake diary. Selected anthropometric measurements were taken using standard techniques. Their Body Mass Index (B.M.I)...
Tipo: Manuscript Palavras-chave: Developmental Biology; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/5009/version/1
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A Tobacco Homolog of DCN1 is Involved in Cellular Reprogramming and in Developmental Transitions Nature Precedings
Julia Hosp; Alexandra Ribarits; Katarzyna Szaszka; Yongfeng Jin; Alisher Tashpulatov; Marina Baumann; Tatiana Resch; Christina Friedmann; Elisabeth Ankele; Viktor Voronin; Klaus Palme; Alisher Touraev; Erwin Heberle-Bors.
Plant proteomes show remarkable plasticity in reaction to environmental challenges and during developmental transitions. Some of this adaptability comes from ubiquitin-mediated protein destruction regulated by cullin-RING E3 ubiquitin ligases (CRLs). CRLs are activated through modification of the cullin subunit with the ubiquitin-like protein RUB/NEDD8 by an E3 ligase called defective in cullin neddylation 1 (DCN1). Here we show that tobacco DCN1 binds ubiquitin and RUB/NEDD8, and associates with cullin. When knocked down by RNAi, tobacco pollen formation stopped and zygotic embryogenesis was blocked around the globular stage. Additionally, we found that RNAi of DCN1 inhibited the stress-triggered reprogramming of cultured microspores from their intrinsic...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/5728/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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ACBD: Database for Ascidian Chemical Genomics Nature Precedings
Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). 

 First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster Palavras-chave: Developmental Biology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/5087/version/1
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ACBD: Database for Ascidian Chemical Genomics Nature Precedings
Yuichiro Hira; Jun Terai; Mitsuru Nakamura; Etsu Tashiro; Masaya Imoto; Kotaro Oka; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database).

First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster Palavras-chave: Developmental Biology; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5087/version/2
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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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Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on Human Fetal Development Nature Precedings
Roxana Moslehi; Caroline Signore; James Troendle; Amiran Dzutsev; James L. Mills.
The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications...
Tipo: Poster Palavras-chave: Developmental Biology; Genetics & Genomics.
Ano: 2009 URL: http://precedings.nature.com/documents/3582/version/1
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Aging as a consequence of misrepair -- A novel theory of aging Nature Precedings
Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2988/version/3
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Aging as a consequence of misrepair -- A novel theory of aging Nature Precedings
Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the original...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2988/version/1
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Aging as a consequence of misrepair -- A novel theory of aging Nature Precedings
Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2988/version/2
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