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Search Results: 1 - 10 of 2841 matches for " Nathan Bahary "
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Gene Duplication of the Zebrafish kit ligand and Partitioning of Melanocyte Development Functions to kit ligand a
Keith A Hultman,Nathan Bahary,Leonard I Zon,Stephen L Johnson
PLOS Genetics , 2007, DOI: 10.1371/journal.pgen.0030017
Abstract: The retention of particular genes after the whole genome duplication in zebrafish has given insights into how genes may evolve through partitioning of ancestral functions. We examine the partitioning of expression patterns and functions of two zebrafish kit ligands, kit ligand a (kitla) and kit ligand b (kitlb), and discuss their possible coevolution with the duplicated zebrafish kit receptors (kita and kitb). In situ hybridizations show that kitla mRNA is expressed in the trunk adjacent to the notochord in the middle of each somite during stages of melanocyte migration and later expressed in the skin, when the receptor is required for melanocyte survival. kitla is also expressed in other regions complementary to kita receptor expression, including the pineal gland, tail bud, and ear. In contrast, kitlb mRNA is expressed in brain ventricles, ear, and cardinal vein plexus, in regions generally not complementary to either zebrafish kit receptor ortholog. However, like kitla, kitlb is expressed in the skin during stages consistent with melanocyte survival. Thus, it appears that kita and kitla have maintained congruent expression patterns, while kitb and kitlb have evolved divergent expression patterns. We demonstrate the interaction of kita and kitla by morpholino knockdown analysis. kitla morphants, but not kitlb morphants, phenocopy the null allele of kita, with defects for both melanocyte migration and survival. Furthermore, kitla morpholino, but not kitlb morpholino, interacts genetically with a sensitized allele of kita, confirming that kitla is the functional ligand to kita. Last, we examine kitla overexpression in embryos, which results in hyperpigmentation caused by an increase in the number and size of melanocytes. This hyperpigmentation is dependent on kita function. We conclude that following genome duplication, kita and kitla have maintained their receptor–ligand relationship, coevolved complementary expression patterns, and that functional analysis reveals that most or all of the kita receptor's function in the embryo are promoted by its interaction with kitla.
Sfrp5 Modulates Both Wnt and BMP Signaling and Regulates Gastrointestinal Organogensis in the Zebrafish, Danio rerio
Carsten Stuckenholz, Lili Lu, Prakash C. Thakur, Tae-Young Choi, Donghun Shin, Nathan Bahary
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062470
Abstract: Sfrp5 belongs to the family of secreted frizzled related proteins (Sfrp), secreted inhibitors of Wingless-MMTV Integration Site (Wnt) signaling, which play an important role in cancer and development. We selected sfrp5 because of its compelling expression profile in the developing endoderm in zebrafish, Danio rerio. In this study, overexpression of sfrp5 in embryos results in defects in both convergent extension (CE) by inhibition of non-canonical Wnt signaling and defects in dorsoventral patterning by inhibition of Tolloid-mediated proteolysis of the BMP inhibitor Chordin. From 25 hours post fertilization (hpf) to 3 days post fertilization (dpf), both overexpression and knockdown of Sfrp5 decrease the size of the endoderm, significantly reducing liver cell number. At 3 dpf, insulin-positive endodermal cells fail to coalesce into a single pancreatic islet. We show that Sfrp5 inhibits both canonical and non-canonical Wnt signaling during embryonic and endodermal development, resulting in endodermal abnormalities.
Functional evolution of the vitamin D and pregnane X receptors
Erica J Reschly, Afonso Bainy, Jaco Mattos, Lee R Hagey, Nathan Bahary, Sripal R Mada, Junhai Ou, Raman Venkataramanan, Matthew D Krasowski
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-222
Abstract: Human, mouse, frog, zebrafish, and lamprey VDRs were found to have similar ligand selectivities for vitamin D derivatives. In contrast, using cultured primary hepatocytes, only zebrafish showed evidence of PXR-mediated induction of enzyme expression, with increases in testosterone 6β-hydroxylation activity (a measure of cytochrome P450 3A activity in other species) and flurbiprofen 4-hydroxylation activity (measure of cytochrome P450 2C activity) following exposure to known PXR activators. A separate assay in vivo using zebrafish demonstrated increased hepatic transcription of another PXR target, multidrug resistance gene (ABCB5), following injection of the major zebrafish bile salt, 5α-cyprinol 27-sulfate. The PXR target function, testosterone hydroxylation, was detected in frog and sea lamprey primary hepatocytes, but was not inducible in these two species by a wide range of PXR activators in other animals. Analysis of the sea lamprey draft genome also did not show evidence of a PXR gene.Our results show tight conservation of ligand selectivity of VDRs across vertebrate species from Agnatha to mammals. Using a functional approach, we demonstrate classic PXR-mediated effects in zebrafish, but not in sea lamprey or African clawed frog liver cells. Using a genomic approach, we failed to find evidence of a PXR gene in lamprey, suggesting that VDR may be the original NR1I gene.The vitamin D receptor (VDR, NR1I1) and pregnane X receptor (PXR, NR1I2) are members of the nuclear hormone receptor (NR) superfamily of ligand-activated transcription factors. NRs work in concert with co-activators and co-repressors to regulate gene expression [1-3]. NRs share a modular domain structure, which includes, from N-terminus to C-terminus, a modulatory A/B domain, the DNA-binding domain (DBD; C domain), the hinge D domain, the ligand-binding domain (LBD; E domain) and a variable C-terminal F domain [3].VDRs bind 1α,25-(OH)2-vitamin D3 (calcitriol) with high affinity and mediate classi
The Zebrafish moonshine Gene Encodes Transcriptional Intermediary Factor 1γ, an Essential Regulator of Hematopoiesis
David G. Ransom,Nathan Bahary,Knut Niss,David Traver,Caroline Burns,Nikolaus S. Trede,Noelle Paffett-Lugassy,Walter J. Saganic,C. Anthoney Lim,Candace Hersey,Yi Zhou,Bruce A. Barut,Shuo Lin,Paul D. Kingsley,James Palis,Stuart H. Orkin,Leonard I. Zon
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0020237
Abstract: Hematopoiesis is precisely orchestrated by lineage-specific DNA-binding proteins that regulate transcription in concert with coactivators and corepressors. Mutations in the zebrafish moonshine (mon) gene specifically disrupt both embryonic and adult hematopoiesis, resulting in severe red blood cell aplasia. We report that mon encodes the zebrafish ortholog of mammalian transcriptional intermediary factor 1γ (TIF1γ) (or TRIM33), a member of the TIF1 family of coactivators and corepressors. During development, hematopoietic progenitor cells in mon mutants fail to express normal levels of hematopoietic transcription factors, including gata1, and undergo apoptosis. Three different mon mutant alleles each encode premature stop codons, and enforced expression of wild-type tif1γ mRNA rescues embryonic hematopoiesis in homozygous mon mutants. Surprisingly, a high level of zygotic tif1γ mRNA expression delineates ventral mesoderm during hematopoietic stem cell and progenitor formation prior to gata1 expression. Transplantation studies reveal that tif1γ functions in a cell-autonomous manner during the differentiation of erythroid precursors. Studies in murine erythroid cell lines demonstrate that Tif1γ protein is localized within novel nuclear foci, and expression decreases during erythroid cell maturation. Our results establish a major role for this transcriptional intermediary factor in the differentiation of hematopoietic cells in vertebrates.
The Zebrafish moonshine Gene Encodes Transcriptional Intermediary Factor 1γ, an Essential Regulator of Hematopoiesis
David G Ransom,Nathan Bahary,Knut Niss,David Traver,Caroline Burns,Nikolaus S Trede,Noelle Paffett-Lugassy,Walter J Saganic,C. Anthoney Lim,Candace Hersey,Yi Zhou,Bruce A Barut,Shuo Lin,Paul D Kingsley,James Palis,Stuart H Orkin,Leonard I Zon
PLOS Biology , 2004, DOI: 10.1371/journal.pbio.0020237
Abstract: Hematopoiesis is precisely orchestrated by lineage-specific DNA-binding proteins that regulate transcription in concert with coactivators and corepressors. Mutations in the zebrafish moonshine (mon) gene specifically disrupt both embryonic and adult hematopoiesis, resulting in severe red blood cell aplasia. We report that mon encodes the zebrafish ortholog of mammalian transcriptional intermediary factor 1γ (TIF1γ) (or TRIM33), a member of the TIF1 family of coactivators and corepressors. During development, hematopoietic progenitor cells in mon mutants fail to express normal levels of hematopoietic transcription factors, including gata1, and undergo apoptosis. Three different mon mutant alleles each encode premature stop codons, and enforced expression of wild-type tif1γ mRNA rescues embryonic hematopoiesis in homozygous mon mutants. Surprisingly, a high level of zygotic tif1γ mRNA expression delineates ventral mesoderm during hematopoietic stem cell and progenitor formation prior to gata1 expression. Transplantation studies reveal that tif1γ functions in a cell-autonomous manner during the differentiation of erythroid precursors. Studies in murine erythroid cell lines demonstrate that Tif1γ protein is localized within novel nuclear foci, and expression decreases during erythroid cell maturation. Our results establish a major role for this transcriptional intermediary factor in the differentiation of hematopoietic cells in vertebrates.
Number in Mathematical Cryptography  [PDF]
Nathan Hamlin
Open Journal of Discrete Mathematics (OJDM) , 2017, DOI: 10.4236/ojdm.2017.71003
Abstract: With the challenge of quantum computing ahead, an analysis of number and representation adequate to the task is needed. Some clarifications on the combinatorial nature of representation are presented here; this is related to the foundations of digital representations of integers, and is thus also of interest in clarifying what numbers are and how they are used in pure and applied mathematics. The author hopes this work will help mathematicians and computer scientists better understand the nature of the Generalized Knapsack Code, a lattice-based code which the author believes to be particularly promising, and the use of number in computing in general.
Study on Nano Silicon Oxide Growth in Argon Media
Fereydoun Ashrafi,S.A. Babanejad; A. Bahary and M. Norouzi
Research Journal of Applied Sciences, Engineering and Technology , 2010,
Abstract: When an ultra thin Silicon oxide film will been grown thermally on Si substrate, the clean oxide film could not be grown because of native oxide on the substrate and impurities such as carbon. Therefore some methods and experiments have been performed for grow ing SiO2 on Si (111) in presence and in absence of Ar gas at high pressure and high temperature. Experiments show that clean and amorphous nano oxide film could be formed at Ar media. Moreover, the film structures have been studied by using AES (Auger Electron Spectroscopy) and SEM (Scanning Electron Microscopy) techniques.
Communicating the Probabilities of Extreme Surface Temperature Outcomes  [PDF]
Nathan Rive, Gunnar Myhre
Atmospheric and Climate Sciences (ACS) , 2012, DOI: 10.4236/acs.2012.24049
Abstract: The magnitude of the future global warming is uncertain, but the possible dramatic changes associated with high temperatures have seen rising attention in the literature. Projections of temperature change in the literature are often presented in probabilistic terms and typically highlight the most likely ranges of future temperature under assumed emission scenarios. However, focusing on these high probability outcomes of global warming omits important information related to the threats of low-probability but high-impact outcomes under more extreme change. As such, we argue that the literature should place more emphasis on communicating the probabilities of extreme temperature change, in a way that is accessible to policymakers and the general public. The damage associated with climate change is likely to be non-linear with temperature, and thus extreme temperature changes may pose a larger risk than the most likely outcomes. We use a simple climate model to explore the probabilities of high surface temperature under business as usual emissions scenarios, given current knowledge of the climate system. In a business as usual scenario (A1FI) we find the probability of “likely” warming (central 66%) to be approximately 4.4°C-6.9°C in 2100 (above 1900 levels). However, we find extreme (>7°C) warming to embody a notable portion of damage risk compared to this likely range.
Community Detection in Dynamic Social Networks  [PDF]
Nathan Aston, Wei Hu
Communications and Network (CN) , 2014, DOI: 10.4236/cn.2014.62015
Abstract:

There are many community detection algorithms for discovering communities in networks, but very few deal with networks that change structure. The SCAN (Structural Clustering Algorithm for Networks) algorithm is one of these algorithms that detect communities in static networks. To make SCAN more effective for the dynamic social networks that are continually changing their structure, we propose the algorithm DSCAN (Dynamic SCAN) which improves SCAN to allow it to update a local structure in less time than it would to run SCAN on the entire network. We also improve SCAN by removing the need for parameter tuning. DSCAN, tested on real world dynamic networks, performs faster and comparably to SCAN from one timestamp to another, relative to the size of the change. We also devised an approach to genetic algorithms for detecting communities in dynamic social networks, which performs well in speed and modularity.

Closing the Gap in Undergraduate Supply Chain Education through Live Experiential Learning  [PDF]
Sime Curkovic, Nathan Fernandez
American Journal of Industrial and Business Management (AJIBM) , 2016, DOI: 10.4236/ajibm.2016.66064
Abstract: With the supply chain industry suffering from a lack of available managerial talent, U.S. companies are stepping up efforts to recruit qualified and skilled professionals from universities. The supply chain industry will need to fill about 1.4 million new jobs over the next four years, but there are concerns regarding where the talent will come from given that demand greatly exceeds supply. The U.S. Bureau of Labor Statistics predicts that employment for supply chain management will increase by 20 percent through 2018, which is nearly twice as fast as the 11 percent average for all industries combined. The Georgia Center of Innovation also reports that the U.S. will be short one million supply chain workers in 2016 alone. Related to the talent shortage, industry has also made clear that they are struggling to evolve their supply chain processes to match business needs. Nearly a third of all supply chain processes are inadequate, according to research from Crimson & Co. In response to these industry demands, Western Michigan University’s Integrated Supply Management Program has placed a strong focus on process management through lean problem-solving techniques. This paper reflects on the industry factors that are currently hampering the process of matching new college graduates with professional positions. It also describes how WMU’s ISM undergraduate program is successfully bridging those gaps and preparing its students by partnering with local businesses on live experiential learning projects.
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