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Nipam Patel

Professor
nipam@uchicago.edu
Research Summary
Over the past two decades, developmental biologists have made great strides in understanding embryonic pattern formation at the genetic, molecular, and cellular levels. Much of this advancement can be attributed to the remarkable success of studies of pattern formation in model systems, such as the fruit fly Drosophila melanogaster. Identification of genes that play major roles in setting up the body plan, combined with the subsequent discovery that many of these genes are well conserved even between different phyla, has also led to a renaissance in the investigation of the links between evolution and development. Using information collected from studies of Drosophila development, my lab and others are beginning to explore the degree to which developmental pathways have been conserved or altered between various arthropods. Insights into the nature of developmental and molecular alterations will help us to understand the evolutionary changes in the mechanisms of pattern formation and provide a molecular basis for analyzing the diversification of body morphologies and developmental mechanisms.
Biosciences Graduate Program Association
Publications

  1. Dual Functions of labial Resolve the Hox Logic of Chelicerate Head Segments. Mol Biol Evol. 2023 03 04; 40(3). View in: PubMed

  2. The BET inhibitor/degrader ARV-825 prolongs the growth arrest response to Fulvestrant + Palbociclib and suppresses proliferative recovery in ER-positive breast cancer. Front Oncol. 2022; 12:966441. View in: PubMed

  3. The Daphnia carapace and other novel structures evolved via the cryptic persistence of serial homologs. Curr Biol. 2022 09 12; 32(17):3792-3799.e3. View in: PubMed

  4. Expression of Abdominal-B in the brine shrimp, Artemia franciscana, expands our evolutionary understanding of the crustacean abdomen. Dev Biol. 2022 09; 489:178-184. View in: PubMed

  5. Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis. Development. 2022 06 01; 149(11). View in: PubMed

  6. The crustacean model Parhyale hawaiensis. Curr Top Dev Biol. 2022; 147:199-230. View in: PubMed

  7. Mimicry can drive convergence in structural and light transmission features of transparent wings in Lepidoptera. Elife. 2021 12 21; 10. View in: PubMed

  8. Developmental, cellular and biochemical basis of transparency in clearwing butterflies. J Exp Biol. 2021 05 15; 224(10). View in: PubMed

  9. Developmental, cellular, and biochemical basis of transparency in clearwing butterflies. J Exp Biol. 2021 May 10. View in: PubMed

  10. Autophagy and senescence in cancer therapy. Adv Cancer Res. 2021; 150:1-74. View in: PubMed

  11. N-acylethanolamine-hydrolysing acid amidase: A new potential target to treat paclitaxel-induced neuropathy. Eur J Pain. 2021 07; 25(6):1367-1380. View in: PubMed

  12. Targeting Peroxisome Proliferator-Activated Receptor-a (PPAR- a) to reduce paclitaxel-induced peripheral neuropathy. Brain Behav Immun. 2021 03; 93:172-185. View in: PubMed

  13. A Fenofibrate Diet Prevents Paclitaxel-Induced Peripheral Neuropathy in Mice. Cancers (Basel). 2020 Dec 29; 13(1). View in: PubMed

  14. Knockout of crustacean leg patterning genes suggests that insect wings and body walls evolved from ancient leg segments. Nat Ecol Evol. 2020 12; 4(12):1703-1712. View in: PubMed

  15. Triangular Relationship between p53, Autophagy, and Chemotherapy Resistance. Int J Mol Sci. 2020 Nov 26; 21(23). View in: PubMed

  16. The Roles of Autophagy and Senescence in the Tumor Cell Response to Radiation. Radiat Res. 2020 08 01; 194(2):103-115. View in: PubMed

  17. Structural color in Junonia butterflies evolves by tuning scale lamina thickness. Elife. 2020 04 07; 9. View in: PubMed

  18. Influence of nonprotective autophagy and the autophagic switch on sensitivity to cisplatin in non-small cell lung cancer cells. Biochem Pharmacol. 2020 05; 175:113896. View in: PubMed

  19. Studies of Non-Protective Autophagy Provide Evidence that Recovery from Therapy-Induced Senescence is Independent of Early Autophagy. Int J Mol Sci. 2020 02 20; 21(4). View in: PubMed

  20. The amphipod crustacean Parhyale hawaiensis: An emerging comparative model of arthropod development, evolution, and regeneration. Wiley Interdiscip Rev Dev Biol. 2019 09; 8(5):e355. View in: PubMed

  21. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. Gigascience. 2019 05 01; 8(5). View in: PubMed

  22. Gallium, neon and helium focused ion beam milling of thin films demonstrated for polymeric materials: study of implantation artifacts. Nanoscale. 2019 Jan 17; 11(3):1403-1409. View in: PubMed

  23. Differential Radiation Sensitivity in p53 Wild-Type and p53-Deficient Tumor Cells Associated with Senescence but not Apoptosis or (Nonprotective) Autophagy. Radiat Res. 2018 11; 190(5):538-557. View in: PubMed

  24. Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms. J Vis Exp. 2018 05 25; (135). View in: PubMed

  25. Monoacylglycerol Lipase Inhibitors Reverse Paclitaxel-Induced Nociceptive Behavior and Proinflammatory Markers in a Mouse Model of Chemotherapy-Induced Neuropathy. J Pharmacol Exp Ther. 2018 07; 366(1):169-183. View in: PubMed

  26. Macroevolutionary shifts of WntA function potentiate butterfly wing-pattern diversity. Proc Natl Acad Sci U S A. 2017 10 03; 114(40):10701-10706. View in: PubMed

  27. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. Elife. 2016 11 16; 5. View in: PubMed

  28. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata). Genome Biol Evol. 2016 06 03; 8(5):1571-89. View in: PubMed

  29. CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution. Curr Biol. 2016 Jan 11; 26(1):14-26. View in: PubMed

  30. An interview with Nipam Patel. Development. 2015 Dec 15; 142(24):4189-90. View in: PubMed

  31. Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis. Dev Biol. 2016 Jan 01; 409(1):297-309. View in: PubMed

  32. A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. PLoS One. 2015; 10(10):e0140484. View in: PubMed

  33. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet. 2015; 16:103-31. View in: PubMed

  34. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics. 2014 Nov 19; 15:350. View in: PubMed

  35. Dynamics of F-actin prefigure the structure of butterfly wing scales. Dev Biol. 2014 Aug 15; 392(2):404-18. View in: PubMed

  36. Multiple recent co-options of Optix associated with novel traits in adaptive butterfly wing radiations. Evodevo. 2014 Feb 05; 5(1):7. View in: PubMed

  37. What is a segment? Evodevo. 2013 Dec 17; 4(1):35. View in: PubMed

  38. Reduction of germ cells in the Odysseus null mutant causes male fertility defect in Drosophila melanogaster. Genes Genet Syst. 2012; 87(4):273-6. View in: PubMed

  39. Independent migration of cell populations in the early gastrulation of the amphipod crustacean Parhyale hawaiensis. Dev Biol. 2012 Nov 01; 371(1):94-109. View in: PubMed

  40. Evolutionary crossroads in developmental biology. Development. 2012 Aug; 139(15):2637-8. View in: PubMed

  41. Evolving specialization of the arthropod nervous system. Proc Natl Acad Sci U S A. 2012 Jun 26; 109 Suppl 1:10634-9. View in: PubMed

  42. Analysis of snail genes in the crustacean Parhyale hawaiensis: insight into snail gene family evolution. Dev Genes Evol. 2012 May; 222(3):139-51. View in: PubMed

  43. The functional relationship between ectodermal and mesodermal segmentation in the crustacean, Parhyale hawaiensis. Dev Biol. 2012 Jan 15; 361(2):427-38. View in: PubMed

  44. Recent advances in crustacean genomics. Integr Comp Biol. 2008 Dec; 48(6):852-68. View in: PubMed

  45. Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticus. Proc Natl Acad Sci U S A. 2011 Apr 05; 108(14):5702-7. View in: PubMed

  46. A prominent requirement for single-minded and the ventral midline in patterning the dorsoventral axis of the crustacean Parhyale hawaiensis. Development. 2010 Oct; 137(20):3469-76. View in: PubMed

  47. BAC library for the amphipod crustacean, Parhyale hawaiensis. Genomics. 2010 May; 95(5):261-7. View in: PubMed

  48. giant is a bona fide gap gene in the intermediate germband insect, Oncopeltus fasciatus. Development. 2010 Mar; 137(5):835-44. View in: PubMed

  49. In situ hybridization of labeled RNA probes to fixed Parhyale hawaiensis embryos. Cold Spring Harb Protoc. 2009 Jan; 2009(1):pdb.prot5130. View in: PubMed

  50. Antibody staining of Parhyale hawaiensis embryos. Cold Spring Harb Protoc. 2009 Jan; 2009(1):pdb.prot5129. View in: PubMed

  51. Injection of Parhyale hawaiensis blastomeres with fluorescently labeled tracers. Cold Spring Harb Protoc. 2009 Jan; 2009(1):pdb.prot5128. View in: PubMed

  52. Fixation and dissection of Parhyale hawaiensis embryos. Cold Spring Harb Protoc. 2009 Jan; 2009(1):pdb.prot5127. View in: PubMed

  53. The crustacean Parhyale hawaiensis: a new model for arthropod development. Cold Spring Harb Protoc. 2009 Jan; 2009(1):pdb.emo114. View in: PubMed

  54. Developmental biology: Asymmetry with a twist. Nature. 2009 Dec 10; 462(7274):727-8. View in: PubMed

  55. Mesoderm and ectoderm lineages in the crustacean Parhyale hawaiensis display intra-germ layer compensation. Dev Biol. 2010 May 01; 341(1):256-66. View in: PubMed

  56. Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean. Proc Natl Acad Sci U S A. 2009 Aug 18; 106(33):13897-902. View in: PubMed

  57. Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology. Proc Natl Acad Sci U S A. 2009 Aug 18; 106(33):13892-6. View in: PubMed

  58. Genomes and evolution: multidimensional approaches to understanding diversity. Curr Opin Genet Dev. 2008 Dec; 18(6):469-71. View in: PubMed

  59. Nodal signalling is involved in left-right asymmetry in snails. Nature. 2009 Feb 19; 457(7232):1007-11. View in: PubMed

  60. Crustaceans. Curr Biol. 2008 Jul 08; 18(13):R547-50. View in: PubMed

  61. Evolution of coloration patterns. Annu Rev Cell Dev Biol. 2008; 24:425-46. View in: PubMed

  62. Patterns on the insect wing. Curr Opin Genet Dev. 2007 Aug; 17(4):300-8. View in: PubMed

  63. Investigating divergent mechanisms of mesoderm development in arthropods: the expression of Ph-twist and Ph-mef2 in Parhyale hawaiensis. J Exp Zool B Mol Dev Evol. 2008 Jan 15; 310(1):24-40. View in: PubMed

  64. Evolutionary biology: how to build a longer beak. Nature. 2006 Aug 03; 442(7102):515-6. View in: PubMed

  65. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A. 2005 Dec 13; 102(50):18017-22. View in: PubMed

  66. Pax3/7 genes reveal conservation and divergence in the arthropod segmentation hierarchy. Dev Biol. 2005 Sep 01; 285(1):169-84. View in: PubMed

  67. Stages of embryonic development in the amphipod crustacean, Parhyale hawaiensis. Genesis. 2005 Jul; 42(3):124-49. View in: PubMed

  68. Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics. Nature. 2005 Apr 28; 434(7037):1134-8. View in: PubMed

  69. Patterning of the branched head appendages in Schistocerca americana and Tribolium castaneum. Evol Dev. 2004 Nov-Dec; 6(6):402-10. View in: PubMed

  70. Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Mol Biol Evol. 2005 Jan; 22(1):40-50. View in: PubMed

  71. Evolutionary biology: time, space and genomes. Nature. 2004 Sep 02; 431(7004):28-9. View in: PubMed

  72. Gene duplication and speciation in Drosophila: evidence from the Odysseus locus. Proc Natl Acad Sci U S A. 2004 Aug 17; 101(33):12232-5. View in: PubMed

  73. Genomes and evolution. From sequence to organism. Curr Opin Genet Dev. 2003 Dec; 13(6):559-61. View in: PubMed

  74. Even-skipped, acting as a repressor, regulates axonal projections in Drosophila. Development. 2003 Nov; 130(22):5385-400. View in: PubMed

  75. The ancestry of segmentation. Dev Cell. 2003 Jul; 5(1):2-4. View in: PubMed

  76. Playing by pair-rules? Bioessays. 2003 May; 25(5):425-9. View in: PubMed

  77. Nanos plays a conserved role in axial patterning outside of the Diptera. Curr Biol. 2003 Feb 04; 13(3):224-9. View in: PubMed

  78. Cell lineage analysis of the amphipod crustacean Parhyale hawaiensis reveals an early restriction of cell fates. Development. 2002 Dec; 129(24):5789-801. View in: PubMed

  79. Developmental biologists cast a net over sequenced genomes. Genome Biol. 2002 Sep 24; 3(10):REPORTS4032. View in: PubMed

  80. The repressor activity of Even-skipped is highly conserved, and is sufficient to activate engrailed and to regulate both the spacing and stability of parasegment boundaries. Development. 2002 Oct; 129(19):4411-21. View in: PubMed

  81. Analysis of the expression pattern of Mysidium columbiae wingless provides evidence for conserved mesodermal and retinal patterning processes among insects and crustaceans. Dev Genes Evol. 2002 Apr; 212(3):114-23. View in: PubMed

  82. Precision patterning. Nature. 2002 Feb 14; 415(6873):748-9. View in: PubMed

  83. Short, long, and beyond: molecular and embryological approaches to insect segmentation. Annu Rev Entomol. 2002; 47:669-99. View in: PubMed
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