Eye Development in Sepia Officinalis Embryo: What the Uncommon Gene
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Six3 Overexpression Initiates the Formation of Ectopic Retina
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION in the developing eye and ventral forebrain. Recently, in Six3 overexpression initiates Drosophila a member of the Six subclass of homeobox the formation of ectopic retina genes, optix, has been isolated, which by sequence com- parison of the homeobox appears to be the ortholog of Felix Loosli, Sylke Winkler, Six3 (Toy et al. 1998). Functional analysis of optix, how- 1 and Joachim Wittbrodt ever, has not yet been reported. In medaka fish (Oryzias latipes) Six3 is expressed in Sonderforschungsbereich (SFB) Junior Group, Institute for Human Genetics, University of Go¨ ttingen, c/o the anterior-most neuroectoderm at gastrula stages and Max-Planck-Institute (MPI) for Biophysical Chemistry, Am later in the developing retina (Loosli et al. 1998). Mosaic Fassberg, 37077 Go¨ttingen, Germany misexpression of mouse Six3 in small clones, in response to injected plasmid DNA, resulted in the formation of The homeobox gene sine oculis (so) is essential for visual ectopic lenses in the region of the otic vesicle, suggesting system formation in Drosophila. A vertebrate member a decisive role for Six3 during vertebrate lens develop- of the so/Six gene family, Six3, is expressed in the devel- ment (Oliver et al. 1996). Considering the expression of oping eye and forebrain. Injection of Six3 RNA into Six3 in the retinal primordia and the essential role of a medaka fish embryos causes ectopic Pax6 and Rx2 ex- Drosophila homolog, so,inDrosophila eye develop- pression in midbrain and cerebellum, resulting in the ment, we investigated a potential role of Six3 in early formation of ectopic retinal primordia. -
Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897 -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Life in the Fast Lane – from Hunted to Hunter Middle School Version
Life in the Fast Lane: From Hunted to Hunter Lab Activity: Dissection of a Squid-A Cephalopod Middle School Version Lesson by Kevin Goff Squid and octopi are cephalopods [say “SEFF-uh-luh-pods”]. The name means “head-foot,” because these animals have VIDEOS TO WATCH gripping, grasping arms that emerge straight from their heads. Watch this short clip on the Shape of Life At first glance, they seem totally different from every other website to become familiar with basic mollusc anatomy: creature on Earth. But in fact, they are molluscs, closely related • “Mollusc Animation: Abalone Body to snails, slugs, clams, oysters, mussels, and scallops. Like all Plan” (under Animation; 1.5 min) modern day molluscs, cephalopods descended from simple, Note the abalone’s foot, radula, and shell- snail-like ancestors. These ancient snails crept sluggishly on making mantle. These were present in the seafloor over 500 million years ago. Their shells resembled the snail-like ancestor of all molluscs an umbrella, probably to shield them from the sun’s intense ultraviolet radiation. When all sorts of new predators appeared on the scene, with powerful jaws or crushing claws, a thin shell was no match for such weapons. Over time, some snails evolved thicker shells, often coiled and spiky. These heavy shells did a better job of fending off predators, but they came with a price: They were costly to build and a burden to lug around. These snails sacrificed speed for safety. This lifestyle worked fine for many molluscs. And, still today, nearly 90% of all molluscs are heavily armored gastropods that crawl around at a snail’s pace. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
The Pax Gene Family: Highlights from Cephalopods Sandra Navet, Auxane Buresi, Sébastien Baratte, Aude Andouche, Laure Bonnaud-Ponticelli, Yann Bassaglia
The Pax gene family: Highlights from cephalopods Sandra Navet, Auxane Buresi, Sébastien Baratte, Aude Andouche, Laure Bonnaud-Ponticelli, Yann Bassaglia To cite this version: Sandra Navet, Auxane Buresi, Sébastien Baratte, Aude Andouche, Laure Bonnaud-Ponticelli, et al.. The Pax gene family: Highlights from cephalopods. PLoS ONE, Public Library of Science, 2017, 12 (3), pp.e0172719. 10.1371/journal.pone.0172719. hal-01921138 HAL Id: hal-01921138 https://hal.archives-ouvertes.fr/hal-01921138 Submitted on 13 Nov 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE The Pax gene family: Highlights from cephalopods Sandra Navet1☯, Auxane Buresi1☯, SeÂbastien Baratte1,2, Aude Andouche1, Laure Bonnaud-Ponticelli1, Yann Bassaglia1,3* 1 UMR BOREA MNHN/CNRS7208/IRD207/UPMC/UCN/UA, MuseÂum National d'Histoire Naturelle, Sorbonne UniversiteÂs, Paris, France, 2 Univ. Paris Sorbonne-ESPE, Sorbonne UniversiteÂs, Paris, France, 3 Univ. Paris Est CreÂteil-Val de Marne, CreÂteil, France ☯ These authors contributed equally to this work. * [email protected] a1111111111 a1111111111 a1111111111 a1111111111 Abstract a1111111111 Pax genes play important roles in Metazoan development. Their evolution has been exten- sively studied but Lophotrochozoa are usually omitted. -
Octopus Consciousness: the Role of Perceptual Richness
Review Octopus Consciousness: The Role of Perceptual Richness Jennifer Mather Department of Psychology, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; [email protected] Abstract: It is always difficult to even advance possible dimensions of consciousness, but Birch et al., 2020 have suggested four possible dimensions and this review discusses the first, perceptual richness, with relation to octopuses. They advance acuity, bandwidth, and categorization power as possible components. It is first necessary to realize that sensory richness does not automatically lead to perceptual richness and this capacity may not be accessed by consciousness. Octopuses do not discriminate light wavelength frequency (color) but rather its plane of polarization, a dimension that we do not understand. Their eyes are laterally placed on the head, leading to monocular vision and head movements that give a sequential rather than simultaneous view of items, possibly consciously planned. Details of control of the rich sensorimotor system of the arms, with 3/5 of the neurons of the nervous system, may normally not be accessed to the brain and thus to consciousness. The chromatophore-based skin appearance system is likely open loop, and not available to the octopus’ vision. Conversely, in a laboratory situation that is not ecologically valid for the octopus, learning about shapes and extents of visual figures was extensive and flexible, likely consciously planned. Similarly, octopuses’ local place in and navigation around space can be guided by light polarization plane and visual landmark location and is learned and monitored. The complex array of chemical cues delivered by water and on surfaces does not fit neatly into the components above and has barely been tested but might easily be described as perceptually rich. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Transient Activation of Meox1 Is an Early Component of the Gene
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Access to Research and Communications Annals 1 Transient activation of Meox1 is an early component of the gene 2 regulatory network downstream of Hoxa2. 3 4 Pavel Kirilenko1, Guiyuan He1, Baljinder Mankoo2, Moises Mallo3, Richard Jones4, 5 5 and Nicoletta Bobola1,* 6 7 (1) School of Dentistry, Faculty of Medical and Human Sciences, University of 8 Manchester, Manchester, UK. 9 (2) Randall Division of Cell and Molecular Biophysics, King's College London, UK. 10 (3) Instituto Gulbenkian de Ciência, Oeiras, Portugal. 11 (4) Genetic Medicine, Manchester Academic Health Science Centre, Central 12 Manchester University Hospitals NHS Foundation Trust, Manchester, UK. 13 (5) Present address: Department of Biology, University of York, York, UK. 14 15 Running title: Hoxa2 activates Meox1 expression. 16 Keywords: Meox1, Hoxa2, homeodomain, development, mouse 17 *Words Count: Material and Methods: 344; Introduction, Results and Discussion: 18 3679 19 19 * Author for correspondence at: AV Hill Building The University of Manchester Manchester M13 9PT United Kingdom Phone: (+44) 161 3060642 E-mail: [email protected] 1 Abstract 2 Hox genes encode transcription factors that regulate morphogenesis in all animals 3 with bilateral symmetry. Although Hox genes have been extensively studied, their 4 molecular function is not clear in vertebrates, and only a limited number of genes 5 regulated by Hox transcription factors have been identified. Hoxa2 is required for 6 correct development of the second branchial arch, its major domain of expression. 7 We now show that Meox1 is genetically downstream from Hoxa2 and is a direct 8 target. -
SUPPLEMENTARY MATERIAL Bone Morphogenetic Protein 4 Promotes
www.intjdevbiol.com doi: 10.1387/ijdb.160040mk SUPPLEMENTARY MATERIAL corresponding to: Bone morphogenetic protein 4 promotes craniofacial neural crest induction from human pluripotent stem cells SUMIYO MIMURA, MIKA SUGA, KAORI OKADA, MASAKI KINEHARA, HIROKI NIKAWA and MIHO K. FURUE* *Address correspondence to: Miho Kusuda Furue. Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Tel: 81-72-641-9819. Fax: 81-72-641-9812. E-mail: [email protected] Full text for this paper is available at: http://dx.doi.org/10.1387/ijdb.160040mk TABLE S1 PRIMER LIST FOR QRT-PCR Gene forward reverse AP2α AATTTCTCAACCGACAACATT ATCTGTTTTGTAGCCAGGAGC CDX2 CTGGAGCTGGAGAAGGAGTTTC ATTTTAACCTGCCTCTCAGAGAGC DLX1 AGTTTGCAGTTGCAGGCTTT CCCTGCTTCATCAGCTTCTT FOXD3 CAGCGGTTCGGCGGGAGG TGAGTGAGAGGTTGTGGCGGATG GAPDH CAAAGTTGTCATGGATGACC CCATGGAGAAGGCTGGGG MSX1 GGATCAGACTTCGGAGAGTGAACT GCCTTCCCTTTAACCCTCACA NANOG TGAACCTCAGCTACAAACAG TGGTGGTAGGAAGAGTAAAG OCT4 GACAGGGGGAGGGGAGGAGCTAGG CTTCCCTCCAACCAGTTGCCCCAAA PAX3 TTGCAATGGCCTCTCAC AGGGGAGAGCGCGTAATC PAX6 GTCCATCTTTGCTTGGGAAA TAGCCAGGTTGCGAAGAACT p75 TCATCCCTGTCTATTGCTCCA TGTTCTGCTTGCAGCTGTTC SOX9 AATGGAGCAGCGAAATCAAC CAGAGAGATTTAGCACACTGATC SOX10 GACCAGTACCCGCACCTG CGCTTGTCACTTTCGTTCAG Suppl. Fig. S1. Comparison of the gene expression profiles of the ES cells and the cells induced by NC and NC-B condition. Scatter plots compares the normalized expression of every gene on the array (refer to Table S3). The central line -
Giant Pacific Octopus (Enteroctopus Dofleini) Care Manual
Giant Pacific Octopus Insert Photo within this space (Enteroctopus dofleini) Care Manual CREATED BY AZA Aquatic Invertebrate Taxonomic Advisory Group IN ASSOCIATION WITH AZA Animal Welfare Committee Giant Pacific Octopus (Enteroctopus dofleini) Care Manual Giant Pacific Octopus (Enteroctopus dofleini) Care Manual Published by the Association of Zoos and Aquariums in association with the AZA Animal Welfare Committee Formal Citation: AZA Aquatic Invertebrate Taxon Advisory Group (AITAG) (2014). Giant Pacific Octopus (Enteroctopus dofleini) Care Manual. Association of Zoos and Aquariums, Silver Spring, MD. Original Completion Date: September 2014 Dedication: This work is dedicated to the memory of Roland C. Anderson, who passed away suddenly before its completion. No one person is more responsible for advancing and elevating the state of husbandry of this species, and we hope his lifelong body of work will inspire the next generation of aquarists towards the same ideals. Authors and Significant Contributors: Barrett L. Christie, The Dallas Zoo and Children’s Aquarium at Fair Park, AITAG Steering Committee Alan Peters, Smithsonian Institution, National Zoological Park, AITAG Steering Committee Gregory J. Barord, City University of New York, AITAG Advisor Mark J. Rehling, Cleveland Metroparks Zoo Roland C. Anderson, PhD Reviewers: Mike Brittsan, Columbus Zoo and Aquarium Paula Carlson, Dallas World Aquarium Marie Collins, Sea Life Aquarium Carlsbad David DeNardo, New York Aquarium Joshua Frey Sr., Downtown Aquarium Houston Jay Hemdal, Toledo -
Confirmation of Pathogenic Mechanisms by SARS-Cov-2–Host
Messina et al. Cell Death and Disease (2021) 12:788 https://doi.org/10.1038/s41419-021-03881-8 Cell Death & Disease ARTICLE Open Access Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome Francesco Messina 1, Emanuela Giombini1, Chiara Montaldo1, Ashish Arunkumar Sharma2, Antonio Zoccoli3, Rafick-Pierre Sekaly2, Franco Locatelli4, Alimuddin Zumla5, Markus Maeurer6,7, Maria R. Capobianchi1, Francesco Nicola Lauria1 and Giuseppe Ippolito 1 Abstract In the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level, but the mechanisms of interaction between host and SARS-CoV-2, determining the grade of COVID-19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred, applying an explorative algorithm (Random Walk with Restart, RWR) triggered by 28 proteins of SARS-CoV-2. The analysis of PPI allowed to estimate the distribution of SARS-CoV-2 proteins in the host cell. Interactome built around one single viral protein allowed to define a different response, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, the network-based approach highlighted a possible direct action of ORF3a and NS7b to enhancing Bradykinin Storm. This network-based representation of SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; clinical outcomes.