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How Economists Can Get Alife, Leigh Tesfatsion 2016 Iowa State University

How Economists Can Get Alife, Leigh Tesfatsion

Leigh Tesfatsion

What, is "artificial life," or alife for short? And why should economists cafe?" • -As-detailed in the entertaining, monographs by Levy (1992) and =Sigmund (1993), the roots of-alife go at least as far back as the work-of.John von-Neumann, in.the nineteen forties on self-replicating automata.. The establishment of.alife as a distinct field of inquiry, however, must be traced to the first alife conference,lOrganized in 1987iby'Chris Langton at the Los Alamos NationalrLaboratory; see Langton (1989). •


Evolutionary Genomics And Adaptive Evolution Of The Hedgehog Gene Family (Shh, Ihh And Dhh) In Vertebrates, Joana Pereira, Warren E. Johnson, Stephen J. O'Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vitor Vasconcelos, Agostinho Antunes 2016 Universidade do Porto - Portugal

Evolutionary Genomics And Adaptive Evolution Of The Hedgehog Gene Family (Shh, Ihh And Dhh) In Vertebrates, Joana Pereira, Warren E. Johnson, Stephen J. O'Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vitor Vasconcelos, Agostinho Antunes

Stephen O'Brien

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to ...


Associations Of Peripubertal Serum Dioxin And Polychlorinated Biphenyl Concentrations With Pubertal Timing Among Russian Boys, Jane S. Burns, Mary M. Lee, Paige L. Williams, Susan A. Korrick, Oleg Sergeyev, Thuy Lam, Boris Revich, Russ Hauser 2016 Harvard School of Public Health

Associations Of Peripubertal Serum Dioxin And Polychlorinated Biphenyl Concentrations With Pubertal Timing Among Russian Boys, Jane S. Burns, Mary M. Lee, Paige L. Williams, Susan A. Korrick, Oleg Sergeyev, Thuy Lam, Boris Revich, Russ Hauser

Mary M. Lee

BACKGROUND: Dioxins, furans, and polychlorinated biphenyls (PCBs), dioxin-like and nondioxin-like, have been linked to alterations in puberty. OBJECTIVES: We examined the association of peripubertal serum levels of these compounds (and their toxic equivalents (TEQs)) with pubertal onset and maturity among Russian boys enrolled at ages 8-9 years and followed prospectively through ages 17-18 years. METHODS: At enrollment, 473 boys had serum dioxin-like compounds and PCBs measured. At the baseline visit and annually until age 17-18 years, a physician performed pubertal staging [Genitalia (G), Pubarche (P), and testicular volume (TV)]. 315 subjects completed the follow-up visit at 17-18 years of age ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


Suppression Of Ischemia In Arterial Occlusive Disease By Jnk-Promoted Native Collateral Artery Development, Kasmir Ramo, Koichi Sugamura, Siobhan M. Craige, John F. Keaney Jr., Roger J. Davis 2016 University of Massachusetts Medical School

Suppression Of Ischemia In Arterial Occlusive Disease By Jnk-Promoted Native Collateral Artery Development, Kasmir Ramo, Koichi Sugamura, Siobhan M. Craige, John F. Keaney Jr., Roger J. Davis

Davis Lab

Arterial occlusive diseases are major causes of morbidity and mortality. Blood flow to the affected tissue must be restored quickly if viability and function are to be preserved. We report that disruption of the mixed-lineage protein kinase (MLK) - cJun NH2-terminal kinase (JNK) signaling pathway in endothelial cells causes severe blockade of blood flow and failure to recover in the murine femoral artery ligation model of hindlimb ischemia. We show that the MLK-JNK pathway is required for the formation of native collateral arteries that can restore circulation following arterial occlusion. Disruption of the MLK-JNK pathway causes decreased Dll4/Notch signaling, excessive ...


Septate Junction Proteins Play Essential Roles In Morphogenesis Throughout Embryonic Development In Drosophila, Sonia Hall, Robert E. Ward 4th 2016 University of Massachusetts Medical School

Septate Junction Proteins Play Essential Roles In Morphogenesis Throughout Embryonic Development In Drosophila, Sonia Hall, Robert E. Ward 4th

Open Access Articles

The septate junction (SJ) is the occluding junction found in the ectodermal epithelia of invertebrate organisms, and is essential to maintain chemically distinct compartments in epithelial organs, to provide the blood-brain barrier in the nervous system, and to provide an important line of defense against invading pathogens. More than 20 genes have been identified to function in the establishment or maintenance of SJs in Drosophila melanogaster Numerous studies have demonstrated the cell biological function of these proteins in establishing the occluding junction, whereas very few studies have examined further developmental roles for them. Here we examined embryos with mutations in ...


Morpholino-Mediated Knockdown Of Dux4 Toward Facioscapulohumeral Muscular Dystrophy Therapeutics, Jennifer C. J. Chen, Oliver D. King, Yuanfan Zhang, Nicholas P. Clayton, Carrie Spencer, Bruce M. Wentworth, Charles P. Emerson Jr., Kathryn R. Wagner 2016 University of Massachusetts Medical School Worcester

Morpholino-Mediated Knockdown Of Dux4 Toward Facioscapulohumeral Muscular Dystrophy Therapeutics, Jennifer C. J. Chen, Oliver D. King, Yuanfan Zhang, Nicholas P. Clayton, Carrie Spencer, Bruce M. Wentworth, Charles P. Emerson Jr., Kathryn R. Wagner

Cell and Developmental Biology Publications and Presentations

Derepression of DUX4 in skeletal muscle has emerged as a likely cause of pathology in facioscapulohumeral muscular dystrophy (FSHD). Here we report on the use of antisense phosphorodiamidate morpholino oligonucleotides to suppress DUX4 expression and function in FSHD myotubes and xenografts. The most effective was phosphorodiamidate morpholino oligonucleotide FM10, which targets the polyadenylation signal of DUX4. FM10 had no significant cell toxicity, and RNA-seq analyses of FSHD and control myotubes revealed that FM10 down-regulated many transcriptional targets of DUX4, without overt off-target effects. Electroporation of FM10 into FSHD patient muscle xenografts in mice also down-regulated DUX4 and DUX4 targets. These ...


Investigating The Roles Of Δnp63 As A Suppressor Of Migration, Invasion, And Metastasis, Ramon E. Flores Gonzalez 2016 The University of Texas Graduate School of Biomedical Sciences at Houston

Investigating The Roles Of Δnp63 As A Suppressor Of Migration, Invasion, And Metastasis, Ramon E. Flores Gonzalez

UT GSBS Dissertations and Theses (Open Access)

Cancer is one of the leading causes of death and disease in the world. Considerable resources are spent to study and understand cancer, with the hope of developing new treatments and eventually cures that will help millions of people. Efforts to understand cancer are hindered by its inherent complexity and instability. Nonetheless, understanding the basics of tumor development and progression are the key to focused on studying the role of ΔNp63 in cancer, a p53 family member known to be involved in epithelial development, microRNA biogenesis, and stem cell maintenance. Using the strength of in vivo mouse models, we found ...


Dichotomous Key To Pea Aphid (Acyrthosiphon Pisum) Apterous Parthenogenic Instars, Bates College Department of Biology, Daisy Diamond, Daniel Levitis 2016 Bates College

Dichotomous Key To Pea Aphid (Acyrthosiphon Pisum) Apterous Parthenogenic Instars, Bates College Department Of Biology, Daisy Diamond, Daniel Levitis

SCARAB Data Repository

We provide a dichotomous key, with photographs and illustrations, for distinguishing between instars of the pea aphid (Acyrthosiphon pisum) in the developmental pathway leading to the apterous parthenogenetic adult. Lengths of body, antenna and cauda are provided for a sample of each instar.


A Usp28-53bp1-P53-P21 Signaling Axis Arrests Growth After Centrosome Loss Or Prolonged Mitosis, Bramwell G. Lambrus, Vikas Daggubati, Yumi Uetake, Phillip M. Scott, Kevin M. Clutario, Greenfield Sluder, Andrew J. Holland 2016 Johns Hopkins University School of Medicine

A Usp28-53bp1-P53-P21 Signaling Axis Arrests Growth After Centrosome Loss Or Prolonged Mitosis, Bramwell G. Lambrus, Vikas Daggubati, Yumi Uetake, Phillip M. Scott, Kevin M. Clutario, Greenfield Sluder, Andrew J. Holland

Cell and Developmental Biology Publications and Presentations

Precise regulation of centrosome number is critical for accurate chromosome segregation and the maintenance of genomic integrity. In nontransformed cells, centrosome loss triggers a p53-dependent surveillance pathway that protects against genome instability by blocking cell growth. However, the mechanism by which p53 is activated in response to centrosome loss remains unknown. Here, we have used genome-wide CRISPR/Cas9 knockout screens to identify a USP28-53BP1-p53-p21 signaling axis at the core of the centrosome surveillance pathway. We show that USP28 and 53BP1 act to stabilize p53 after centrosome loss and demonstrate this function to be independent of their previously characterized role in ...


Supervillin Is A Component Of The Hair Cell's Cuticular Plate And The Head Plates Of Organ Of Corti Supporting Cells, Lana M. Pollock, Nilay Gupta, Xi Chen, Elizabeth J. Luna, Brian M. McDermott Jr 2016 Case Western Reserve University

Supervillin Is A Component Of The Hair Cell's Cuticular Plate And The Head Plates Of Organ Of Corti Supporting Cells, Lana M. Pollock, Nilay Gupta, Xi Chen, Elizabeth J. Luna, Brian M. Mcdermott Jr

Cell and Developmental Biology Publications and Presentations

The organ of Corti has evolved a panoply of cells with extraordinary morphological specializations to harness, direct, and transduce mechanical energy into electrical signals. Among the cells with prominent apical specializations are hair cells and nearby supporting cells. At the apical surface of each hair cell is a mechanosensitive hair bundle of filamentous actin (F-actin)-based stereocilia, which insert rootlets into the F-actin meshwork of the underlying cuticular plate, a rigid organelle considered to hold the stereocilia in place. Little is known about the protein composition and development of the cuticular plate or the apicolateral specializations of organ of Corti ...


Osteopetrorickets Due To Snx10 Deficiency In Mice Results From Both Failed Osteoclast Activity And Loss Of Gastric Acid-Dependent Calcium Absorption, Liang Ye, Leslie R. Morse, Li Zhang, Hajime Sasaki, Jason C. Mills, Paul R. Odgren, Greg Sibbel, James R.L. Stanley, Gee Wong, Ariane Zamarioli, Ricardo A. Battaglino 2016 The Forsyth Institute

Osteopetrorickets Due To Snx10 Deficiency In Mice Results From Both Failed Osteoclast Activity And Loss Of Gastric Acid-Dependent Calcium Absorption, Liang Ye, Leslie R. Morse, Li Zhang, Hajime Sasaki, Jason C. Mills, Paul R. Odgren, Greg Sibbel, James R.L. Stanley, Gee Wong, Ariane Zamarioli, Ricardo A. Battaglino

Paul R. Odgren PhD

Mutations in sorting nexin 10 (Snx10) have recently been found to account for roughly 4% of all human malignant osteopetrosis, some of them fatal. To study the disease pathogenesis, we investigated the expression of Snx10 and created mouse models in which Snx10 was knocked down globally or knocked out in osteoclasts. Endocytosis is severely defective in Snx10-deficient osteoclasts, as is extracellular acidification, ruffled border formation, and bone resorption. We also discovered that Snx10 is highly expressed in stomach epithelium, with mutations leading to high stomach pH and low calcium solubilization. Global Snx10-deficiency in mice results in a combined phenotype: osteopetrosis ...


Myc And Fgf Are Required For Zebrafish Neuromast Hair Cell Regeneration, Sang Goo Lee, Mingqian Huang, Nikolaus D. Obholzer, Shan Sun, Wenyan Li, Marco Petrillo, Pu Dai, Yi Zhou, Douglas A. Contanche, Sean G. Megason, Huawei Li, Zheng-Yi Chen 2016 Harvard Medical School

Myc And Fgf Are Required For Zebrafish Neuromast Hair Cell Regeneration, Sang Goo Lee, Mingqian Huang, Nikolaus D. Obholzer, Shan Sun, Wenyan Li, Marco Petrillo, Pu Dai, Yi Zhou, Douglas A. Contanche, Sean G. Megason, Huawei Li, Zheng-Yi Chen

Cell and Developmental Biology Publications and Presentations

Unlike mammals, the non-mammalian vertebrate inner ear can regenerate the sensory cells, hair cells, either spontaneously or through induction after hair cell loss, leading to hearing recovery. The mechanisms underlying the regeneration are poorly understood. By microarray analysis on a chick model, we show that chick hair cell regeneration involves the activation of proliferation genes and downregulation of differentiation genes. Both MYC and FGF are activated in chick hair cell regeneration. Using a zebrafish lateral line neuromast hair cell regeneration model, we show that the specific inhibition of Myc or Fgf suppresses hair cell regeneration, demonstrating that both pathways are ...


The Role Of Nadph Oxidase In Ros Mediated Differentiation, Benjamin J. Dickson 2016 The University of Western Ontario

The Role Of Nadph Oxidase In Ros Mediated Differentiation, Benjamin J. Dickson

Electronic Thesis and Dissertation Repository

Mouse teratocarcinoma F9 cells differentiate into primitive endoderm (PrE) when treated with retinoic acid (RA) or H2O2 and these changes are accompanied by an upregulation of Wnt6 and activation of the canonical WNT/β-catenin pathway. Data from our lab shows PrE differentiation is accompanied by an increase in reactive oxygen species (ROS), which induces a conformational change in Nucleoredoxin preventing its ability to bind and inhibit Dishevelled. This in turn positively impacts on the WNT/β- catenin signaling pathway leading to differentiation. The source of endogenous ROS seen following RA treatment was investigated and members of the NADPH oxidase (NOX ...


Promoter-Enhancer Looping At The Pparγ2 Locus During Adipogenic Differentiation Requires The Prmt5 Methyltransferase, Scott E. LeBlanc, Qiong Wu, Pallavi Lamba, Said Sif, Anthony N. Imbalzano 2016 University of Massachusetts Medical School

Promoter-Enhancer Looping At The Pparγ2 Locus During Adipogenic Differentiation Requires The Prmt5 Methyltransferase, Scott E. Leblanc, Qiong Wu, Pallavi Lamba, Said Sif, Anthony N. Imbalzano

Imbalzano Lab

PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-dependent loop between the PPARγ2 promoter and an enhancer sequence 10 kb upstream that forms at the onset of PPARγ2 expression. The arginine methyltransferase Prmt5 was required for loop formation, and overexpression of Prmt5 resulted in premature loop formation and earlier onset of PPARγ2 expression. Kinetic studies of regulatory factor interactions at the PPARγ2 promoter and enhancer revealed enhanced ...


Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris 2016 MRC Harwell

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we ...


Modelling The Polarization, Migration And Neuromast Deposition In The Zebrafish Posterior Lateral Line System, Hildur Knutsdottir 2016 University of British Columbia

Modelling The Polarization, Migration And Neuromast Deposition In The Zebrafish Posterior Lateral Line System, Hildur Knutsdottir

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Tracheal Occlusion In The Embryonic Lung, Uduak George 2016 University of Louisiana Monroe

Modeling Tracheal Occlusion In The Embryonic Lung, Uduak George

Biology and Medicine Through Mathematics Conference

No abstract provided.


Translating Dosage Compensation To Trisomy 21, Jun Jiang, Yuanchun Jing, Gregory J. Cost, Jen-Chieh Chiang, Heather J. Kolpa, Allison M. Cotton, Dawn M. Carone, Benjamin R. Carone, Meg Byron, Philip D. Gregory, Carolyn J. Brown, Fyodor D. Urnov, Lisa L. Hall, Jeanne B. Lawrence 2016 University of Massachusetts Medical School

Translating Dosage Compensation To Trisomy 21, Jun Jiang, Yuanchun Jing, Gregory J. Cost, Jen-Chieh Chiang, Heather J. Kolpa, Allison M. Cotton, Dawn M. Carone, Benjamin R. Carone, Meg Byron, Philip D. Gregory, Carolyn J. Brown, Fyodor D. Urnov, Lisa L. Hall, Jeanne B. Lawrence

UMass Center for Clinical and Translational Science Research Retreat

Down syndrome is the leading genetic cause of intellectual disabilities, occurring in 1 out of 700 live births. Given that Down syndrome is caused by an extra copy of chromosome 21 that involves over-expression of 400 genes across a whole chromosome, it precludes any possibility of a genetic therapy. Our lab has long studied the natural dosage compensation mechanism for X chromosome inactivation. To “dosage compensate” X-linked genes between females and males, the X-linked XIST gene produces a large non-coding RNA that silences one of the two X chromosomes in female cells. The initial motivation of this study was to ...


Associations Of Peripubertal Serum Dioxin And Polychlorinated Biphenyl Concentrations With Pubertal Timing Among Russian Boys, Jane S. Burns, Mary M. Lee, Paige L. Williams, Susan A. Korrick, Oleg Sergeyev, Thuy Lam, Boris Revich, Russ Hauser 2016 Harvard School of Public Health

Associations Of Peripubertal Serum Dioxin And Polychlorinated Biphenyl Concentrations With Pubertal Timing Among Russian Boys, Jane S. Burns, Mary M. Lee, Paige L. Williams, Susan A. Korrick, Oleg Sergeyev, Thuy Lam, Boris Revich, Russ Hauser

Cell and Developmental Biology Publications and Presentations

BACKGROUND: Dioxins, furans, and polychlorinated biphenyls (PCBs), dioxin-like and nondioxin-like, have been linked to alterations in puberty.

OBJECTIVES: We examined the association of peripubertal serum levels of these compounds (and their toxic equivalents (TEQs)) with pubertal onset and maturity among Russian boys enrolled at ages 8-9 years and followed prospectively through ages 17-18 years.

METHODS: At enrollment, 473 boys had serum dioxin-like compounds and PCBs measured. At the baseline visit and annually until age 17-18 years, a physician performed pubertal staging [Genitalia (G), Pubarche (P), and testicular volume (TV)]. 315 subjects completed the follow-up visit at 17-18 years of age ...


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