Gastrointestinal Tract Development

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The early gastrointestinal tract.
Human head (Week 4, Stage 11) showing buccopharyngeal membrane breakdown.

The gastrointestinal tract (GIT) arises initially during the process of gastrulation from the endoderm of the trilaminar embryo (week 3) and extends from the buccopharyngeal membrane to the cloacal membrane. The tract and associated organs later have contributions from all the germ cell layers.

During the 4th week three distinct regions (fore-, mid- and hind-gut) extend the length of the embryo and will contribute different components of the GIT. The large mid-gut is generated by lateral embryonic folding which "pinches off" a pocket of the yolk sac, the 2 compartments continue to communicate through the vitelline duct.

The oral cavity (mouth) is formed following breakdown of the buccopharyngeal membrane (oropharyngeal or oral membrane) and contributed to mainly by the pharynx lying within the pharyngeal arches (More? Head Development). Loss of buccopharyngeal membrane opens the tract to amniotic fluid through the remainder of development, and during the fetal period is actively swallowed.

From the oral cavity the next portion of the foregut is initially the pharynx, a single gastrointestinal (oesophagus) and respiratory (trachea) common tube, that lies behind the heart. Note that the respiratory tract will form from a ventral bud arising at this level (More? Respiratory).

This current page provides an introductory overview, use the links below for descriptions of specific components and regions as well as developmental abnormalities.

GIT Links: Introduction | Medicine Lecture | Science Lecture | Endoderm | Stomach | Liver | Gall Bladder | Pancreas | Intestine | Tongue | Taste | Enteric Nervous System | Stage 13 | Stage 22 | Abnormalities | Movies | Postnatal | Milk | Tooth | Tongue | BGD Lecture | BGD Practical | Category:Gastrointestinal Tract
GIT Histology Links: Upper GIT | Salivary Gland | Smooth Muscle Histology | Liver | Gall Bladder | Pancreas | Colon | Histology Stains | Histology | GIT Development
Historic Embryology
1878 Alimentary Canal | 1882 The Organs of the Inner Germ-Layer The Alimentary Tube with its Appended Organs | 1902 The Organs of Digestion | 1906 Liver | 1907 Development of the Digestive System | 1907 Atlas | 1907 23 Somite Embryo | 1912 Digestive Tract | 1917 Entodermal Canal | 1918 Anatomy | 1921 Alimentary Tube | 2014 GIT Notes | Historic Disclaimer
Human Embryo: 1908 13-14 Somite Embryo | 1926 22 Somite Embryo | 1907 23 Somite Embryo | 1937 25 Somite Embryo | 1914 27 Somite Embryo | 1914 Week 7 Embryo
Animal Development: 1913 Chicken | 1951 Frog

Note that in historic texts the term entoderm is used to describe endoderm and other terminology may also differ from current descriptions.

Some Recent Findings

Early endoderm development
  • Three-dimensional reconstructions of intrahepatic bile duct tubulogenesis in human liver[1] In the developing human liver, three-dimensional reconstructions using multiple marker proteins confirmed that the human intrahepatic biliary tree forms through several developmental stages involving an initial transition of primitive hepatocytes into cholangiocytes shaping the ductal plate followed by a process of maturation and remodeling where the intrahepatic biliary tree develops through an asymmetrical form of cholangiocyte tubulogenesis. Liver Development
  • Endocrine Pancreas[2] "The transcription factor Pax6 functions in the specification and maintenance of the differentiated cell lineages in the endocrine pancreas. It has two DNA binding domains, the paired domain and the homeodomain, in addition to a C-terminal transactivation domain. The phenotype of Pax6-/- knockout mice suggests non-redundant functions of the transcription factor in the development of glucagon-expressing alpha-cells as this cell type is absent in the mutants."
More recent papers
Mark Hill.jpg
This table shows an automated computer PubMed search using the listed sub-heading term.
  • Therefore the list of references do not reflect any editorial selection of material based on content or relevance.
  • References appear in this list based upon the date of the actual page viewing.

References listed on the rest of the content page and the associated discussion page (listed under the publication year sub-headings) do include some editorial selection based upon both relevance and availability.

Links: References | Discussion Page | Pubmed Most Recent | Journal Searches

Search term: Gastrointestinal Tract Embryology

Raúl Contreras, Job Rodríguez Hernández IMAGES IN CLINICAL MEDICINE. Megaduodenum in Systemic Sclerosis. N. Engl. J. Med.: 2015, 373(17);e20 PubMed 26488715

Mehmet F Sönmez, Derya Karabulut, Yusuf Gunduz, Munis Dundar The Effects of Long-Term Diabetes on Ghrelin Expression in Rat Stomachs. Adv Clin Exp Med: 2015, 24(3);401-7 PubMed 26467127

Reijo Luoma [Respiratory insufficiency due to duplications of the oesophagus]. [Ruokatorven kahdentuman aiheuttama hengitysvajaus.] Duodecim: 2015, 131(15);1376-8 PubMed 26427237

Tulika Tripathi, Neha, Shubhra Gill, Priyank Rai Multidisciplinary Rehabilitation in a Case of Congenital Aglossia with Situs Inversus Totalis. Int J Orthod Milwaukee: 2015, 26(2);39-43 PubMed 26349289

I Ertugrul, V Dogan, S Beken, S Ozgur, N Okumuş, U A Orün, S Karademir UHL'S ANOMALY AS A PART OF VACTERL ASSOCIATION. Genet. Couns.: 2015, 26(2);273-6 PubMed 26349203


  • Human Embryology Larson Chapter 9 p229-260
  • The Developing Human: Clinically Oriented Embryology (6th ed.) Moore and Persaud Chapter 12 p271-302
  • Before We Are Born (5th ed.) Moore and Persaud Chapter 13 p255-287
  • Essentials of Human Embryology Larson Chapter 9 p123-146
  • Human Embryology Fitzgerald and Fitzgerald Chapter 19,20 p119-123

More? References | Online Textbooks | Historic Textbooks

UNSW Students
Mark Hill icon.jpg You have access the following online Embryology textbooks through the UNSW Library.
The Developing Human, 8th edn.jpg Moore, K.L. & Persuad, T.V.N. (2008). The Developing Human: clinically oriented embryology (8th ed.). Philadelphia: Saunders.
Larsen's human embryology 4th edn.jpg Schoenwolf, G.C., Bleyl, S.B., Brauer, P.R. and Francis-West, P.H. (2009). Larsen’s Human Embryology (4th ed.). New York; Edinburgh: Churchill Livingstone.


  • Understanding of germ layer contributions to the early gastrointestinal tract (GIT)
  • Understanding of the folding of the GIT
  • Understanding of three main GIT embryonic divisions
  • Understanding of associated organ development (liver, pancreas, spleen)
  • Brief understanding of mechanical changes (rotations) during GIT development
  • Brief understanding of gastrointestinal abnormalities

Germ Layer Contributions

  • Endoderm - epithelium and associated glands
  • Mesoderm (splanchnic) - mesentry, connective tissues, smooth muscle, blood vessels
  • Ectoderm (neural crest) - enteric nervous system (neural tube) - extrinsic innervation

Both endoderm and mesoderm will contribute to associated organs.

Gastrointestinal Tract Movies

GIT Cartoons
Mesoderm 001 icon.jpg
 ‎‎Week 3 Mesoderm
Page | Play
Endoderm 002 icon.jpg
Page | Play
Gastrointestinal tract growth 01 icon.jpg
 ‎‎Tract Growth
Page | Play
Stomach rotation 01 icon.jpg
 ‎‎Stomach Rotation
Page | Play
Lesser sac 01 icon.jpg
 ‎‎Lesser sac
Page | Play
Greater omentum 001 icon.jpg
 ‎‎Greater Omentum
Page | Play

3 GIT divisions

GIT blood supply.jpg
During the 4th week the 3 distinct portions (fore-, mid- and hind-gut) extend the length of the embryo and will contribute different components of the GIT. These 3 divisions are also later defined by the vascular (artery) supply to each of theses divisions.

The large mid-gut is generated by lateral embryonic folding which "pinches off" a pocket of the yolk sac, the 2 compartments continue to communicate through the vitelline duct.

The oral cavity (mouth) is formed following breakdown of the buccopharyngeal membrane (oropharyngeal, oral membrane) and contributed to mainly by the pharynx lying within the pharyngeal arches. The opening of the GIT means that it contains amniotic fluid, which is also swallowed later in development.


Stage 11 foregut
From the oral cavity the next portion of the foregut is initially a single gastrointestinal (oesophagus) and respiratory (trachea) common tube, the pharynx which lies behind the heart. Note that the respiratory tract will form from a ventral bud arising at this level.
  • Oral cavity
  • Pharynx (esophagus, trachea)
  • Respiratory tract
  • Stomach


midgut herniation

From beneath the stomach the initial portion of the small intestine, the duodenum, and the associated pancreas now lie.

Much of the midgut is herniated at the umbilicus external to the abdomen through development. A key step in development is the rotation of this midgut that must occur to place the GIT in the correct abdominal position with its associated mesentry. The GIT itself differentiates to form significantly different structures along its length: oesophagus, stomach, duodenum, jejunum, iliem (small intestine), colon (large intestine).

The mesentries of the GIT are generated from the common dorsal mesentry, with the ventral mesentry contributing to the lesser omentum and falciform ligament.


The distral transverse colon, descending colon, sigmoid colon, rectum and cloaca. The cloaca is the common urogenital sinus which will later become partitioned into an anterior urinary and posterior GIT rectal component.

Links: Intestine Development

Development Overview

GIT shown in green anchored by dosal and ventral mesogastrium. The space ouside this will be the peritoneal cavity.

Red ring-neural tube with neural crestBlue ring- notocordOrange- somites

Differentiation of associated organs at the level of the forming stomach occurs both dorsally (spleen) and ventrally (liver).


Large blue ring- dorsal aortaDark green ring- Liver

Continued growth of the GIT and the organs leads to organ movements and bending of tract.

Carnegie stage 13 Embryo Overview

Below is an overview of the sections starting at the level of pharynx compressed dorsoventrally, following the GIT through to the rectum. The most obvious feature is that of a continuous tube initially, attached by dorsoventral mesentry. Outside this tube and mesentry (at the levels below the lung buds) is the intraembryonic coelom that will form the peritoneal cavity. The hepatic diverticulum (liver bud) lies under the septum transversum is the earliest associated GIT organ that has differentiated, and now occupies a substantial region of the abdomen. Clicking on sections below will open the original images.

Bifurcation of the pharynx into anterior respiratory and posterior oesophagous. The stomach forming beneath the lung buds and adjacent to the developing liver. Below the stomach the GIT has a large dorsal mesogastrium and finer ventral mesogastrium. Associated with the tract is the large portal blood vessel derived from the vitelline circulation. At the bottom curvature of the embryo the mesentry association with the GIT shows extensive vitelline vessels running out through the umbilicus. The hindgut can then be seen, ending at the common urogenital sinus, the cloaca.


Myenteric plexus lying between the outer two layers of smooth muscle

Neural History

  • 1857 Meissner was the first to describe a nerve plexus in the submucosa of the bowel wall.
  • 1864 Auerbach described the myenteric plexus between the longitudinal and circular muscle layers.
  • 1981 LeDouarin describes neural crest contribution to both plexuses.

Myenteric Plexus

  • Peristalsis
  • Coordinated waves of descending inhibition followed by waves of descending excitation

+ Extrinsic parasympathetic cholinergic nerves (vagal and sacral) excite peristalsis and stimulate

- Sympathetic noradrenergic nerves inhibit the transit of gut contents

Submucosal Plexus

  • epithelial movements
  • secretion and absorption

Associated Organs

Liver, pancreas and spleen (stage 22 embryo).

The early tract develops as a simple tube, then a number of endodermal outgrowths from this tube at different levels and contribute to a range of additional organs and tissues. The gastrointestinal associated organs liver, gall bladder and pancreas. Development of these organs is described on separate pages.

There are also a number of additional non-gastrointestinal structures including the respiratory tract and development within the mesentery such as the spleen.

Links: Liver | Gall Bladder | PancreasLiver Histology | Pancreas Histology | Gall Bladder Histology

Gastrointestinal Tract Abnormalities

Only a brief description is given on this current page, for more details see Gastrointestinal Tract - Abnormalities.

Lumen Abnormalities

There are several types of abnormalities that impact upon the continuity of the gastrointestinal tract lumen.

  • Atresia - interuption of the lumen (esophageal atresia, duodenal atresia, extrahepatic biliary atresia, anorectal atresia)
  • Stenosis - narrowing of the lumen (duodenal stenosis, pyloric stenosis).
  • Duplication - incomplete recanalization resulting in parallel lumens, this is really a specialized form of stenosis.

Meckel's Diverticulum

This GIT abnormality is a very common and results from improper closure and absorption of the omphalomesenteric duct (vitelline duct) in development. This transient developmental duct connects the yolk to the primitive GIT.

Intestinal Malrotation

Intestinal malrotation.jpg

Links: Intestinal Malrotation

Intestinal Aganglionosis

(intestinal aganglionosis, Hirschsprung's disease, aganglionic colon, megacolon, congenital aganglionic megacolon, congenital megacolon) A condition caused by the lack of enteric nervous system (neural ganglia) in the intestinal tract responsible for gastric motility (peristalsis).


Gastroschisis (omphalocele, paraomphalocele, laparoschisis, abdominoschisis, abdominal hernia) is a congenital abdominal wall defect which results in herniation of fetal abdominal viscera (intestines and/or organs) into the amniotic cavity. Incidence of gastroschisis has been reported at 1.66/10,000, occuring more frequently in young mothers (less than 20 years old).

By definition, it is a body wall musculoskeletal defect, not a gastrointestinal tract defect, which in turn impacts upon GIT development.

Links: Gastroschisis | Gastrointestinal Tract - Abnormalities


The endoderm of the developing gastrointestinal tract is a source for patterning signals for both within the tract and also for the surrounding organs and tissues.

  • Sox2 - expressed in the anterior part of the primitive gut[3]
  • Cdx2 - expressed in the posterior part of the primitive gut[3]
  • GDNF - regulate migration of enteric neural crest cells[4]
  • endothelin - regulate migration of enteric neural crest cells[4]


  1. Peter S Vestentoft, Peter Jelnes, Branden M Hopkinson, Ben Vainer, Kjeld Møllgård, Bjørn Quistorff, Hanne C Bisgaard Three-dimensional reconstructions of intrahepatic bile duct tubulogenesis in human liver. BMC Dev. Biol.: 2011, 11;56 PubMed 21943389
  2. Petra Dames, Ramona Puff, Michaela Weise, Klaus G Parhofer, Burkhard Göke, Magdalena Götz, Jochen Graw, Jack Favor, Andreas Lechner Relative roles of the different Pax6 domains for pancreatic alpha cell development. BMC Dev. Biol.: 2010, 10;39 PubMed 20377917
  3. 3.0 3.1 Lalini Raghoebir, Elvira R M Bakker, Jason C Mills, Sigrid Swagemakers, Marjon Buscop-van Kempen, Anne Boerema-de Munck, Siska Driegen, Dies Meijer, Frank Grosveld, Dick Tibboel, Ron Smits, Robbert J Rottier SOX2 redirects the developmental fate of the intestinal epithelium toward a premature gastric phenotype. J Mol Cell Biol: 2012, 4(6);377-85 PubMed 22679103
  4. 4.0 4.1 Akihiro Goto, Kenta Sumiyama, Yuji Kamioka, Eiji Nakasyo, Keisuke Ito, Mitsuhiro Iwasaki, Hideki Enomoto, Michiyuki Matsuda GDNF and endothelin 3 regulate migration of enteric neural crest-derived cells via protein kinase A and Rac1. J. Neurosci.: 2013, 33(11);4901-12 PubMed 23486961

Online Textbooks

Historic Textbooks

Historic Disclaimer - information about historic embryology pages 
Mark Hill.jpg
Pages where the terms "Historic Textbook" and "Historic Embryology" appear on this site, indicate that the content and scientific understanding are specific to the time of publication. This means that while some scientific descriptions are still accurate, the terminology and interpretation of the developmental mechanisms reflect the understanding at the time of original publication and those of the preceding periods, these terms and interpretations may not reflect our current scientific understanding.
(More? Embryology History | Historic Embryology Papers)


Alan J Burns, Rachael R Roberts, Joel C Bornstein, Heather M Young Development of the enteric nervous system and its role in intestinal motility during fetal and early postnatal stages. Semin. Pediatr. Surg.: 2009, 18(4);196-205 PubMed 19782301

Sally F Burn, Robert E Hill Left-right asymmetry in gut development: what happens next? Bioessays: 2009, 31(10);1026-37 PubMed 19708022

Valérie A McLin, Susan J Henning, Milan Jamrich The role of the visceral mesoderm in the development of the gastrointestinal tract. Gastroenterology: 2009, 136(7);2074-91 PubMed 19303014

H M Young On the outside looking in: longitudinal muscle development in the gut. Neurogastroenterol. Motil.: 2008, 20(5);431-3 PubMed 18416699

Deborah C Rubin Intestinal morphogenesis. Curr. Opin. Gastroenterol.: 2007, 23(2);111-4 PubMed 17268237

Josef Neu Gastrointestinal development and meeting the nutritional needs of premature infants. Am. J. Clin. Nutr.: 2007, 85(2);629S-634S PubMed 17284768

Richard B Anderson, Donald F Newgreen, Heather M Young Neural crest and the development of the enteric nervous system. Adv. Exp. Med. Biol.: 2006, 589;181-96 PubMed 17076282

Robert H Costa, Vladimir V Kalinichenko, Ai-Xuan L Holterman, Xinhe Wang Transcription factors in liver development, differentiation, and regeneration. Hepatology: 2003, 38(6);1331-47 PubMed 14647040

P de Santa Barbara, G R van den Brink, D J Roberts Development and differentiation of the intestinal epithelium. Cell. Mol. Life Sci.: 2003, 60(7);1322-32 PubMed 12943221

L R Johnson Functional development of the stomach. Annu. Rev. Physiol.: 1985, 47;199-215 PubMed 3922287


Bettina Wilm, Annemieke Ipenberg, Nicholas D Hastie, John B E Burch, David M Bader The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature. Development: 2005, 132(23);5317-28 PubMed 16284122

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Search Mar 2007 "gastrointestinal tract development" 29,361 reference articles of which 3,494 were reviews.

Search April 2010 "Gastrointestinal Tract Development" - All (35980) Review (4707) Free Full Text (8086)

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Additional Images


Gastrointestinal Tract Development

  • allantois - An extraembryonic membrane, endoderm in origin extension from the early hindgut, then cloaca into the connecting stalk of placental animals, connected to the superior end of developing bladder. In reptiles and birds, acts as a reservoir for wastes and mediates gas exchange. In mammals is associated/incorporated with connecting stalk/placental cord fetal-maternal interface.
  • amnion - An extraembryonic membrane]ectoderm and extraembryonic mesoderm in origin and forms the innermost fetal membrane, produces amniotic fluid. This fluid-filled sac initially lies above the trilaminar embryonic disc and with embryoic disc folding this sac is drawn ventrally to enclose (cover) the entire embryo, then fetus. The presence of this membane led to the description of reptiles, bird, and mammals as amniotes.
  • amniotic fluid - The fluid that fills amniotic cavity totally encloses and cushions the embryo. Amniotic fluid enters both the gastrointestinal and respiratory tract following rupture of the buccopharyngeal membrane. The late fetus swallows amniotic fluid.
  • buccal - (Latin, bucca = cheek) A term used to relate to the mouth (oral cavity).
  • buccopharyngeal membrane - (oral membrane) (Latin, bucca = cheek) A membrane which forms the external upper membrane limit (cranial end) of the early gastrointestinal tract (GIT). This membrane develops during gastrulation by ectoderm and endoderm without a middle (intervening) layer of mesoderm. The membrane lies at the floor of the ventral depression (stomodeum) where the oral cavity will open and will breakdown to form the initial "oral opening" of the gastrointestinal tract. The equivilent membrane at the lower end of the gastrointestinal tract is the cloacal membrane.
  • cloacal membrane - Forms the external lower membrane limit (caudal end) of the early gastrointestinal tract (GIT). This membrane is formed during gastrulation by ectoderm and endoderm without a middle (intervening) layer of mesoderm. The membrane breaks down to form the initial "anal opening" of the gastrointestinal tract.
  • coelom - Term used to describe a space. There are extraembryonic and intraembryonic coeloms that form during vertebrate development. The single intraembryonic coelom will form the 3 major body cavities: pleural, pericardial and peritoneal.
  • foregut - The first of the three part/division (foregut - midgut - hindgut) of the early forming gastrointestinal tract. The foregut runs from the buccopharyngeal membrane to the midgut and forms all the tract (esophagus and stomach) from the oral cavity to beneath the stomach. In addition, a ventral bifurcation of the foregut will also form the respiratory tract epithelium.
  • gastrula - (Greek, gastrula = little stomach) A stage of an animal embryo in which the three germ layers ([E#endoderm|endoderm]/mesoderm/ectoderm) have just formed.
  • gastrulation - The process of differentiation forming a gastrula. Term means literally means "to form a gut" but is more in development, as this process converts the bilaminar embryo (epiblast/hypoblast) into the trilaminar embryo (E#endoderm endoderm/mesoderm/ectoderm) establishing the 3 germ layers that will form all the future tissues of the entire embryo. This process also establishes the the initial body axes.
  • hindgut - The last of the three part/division foregut - midgut - hindgut) of the early forming gastrointestinal tract. The hindgut forms all the tract from the distral transverse colon to the cloacal membrane and extends into the connecting stalk (placental cord) as the allantois. In addition, a ventral of the hindgut will also form the urinary tract (bladder, urethra) epithelium.
  • intraembryonic coelom - The "horseshoe-shaped" space (cavity) that forms initially in the third week of development in the lateral plate mesoderm that will eventually form the 3 main body cavities: pericardial, pleural, peritoneal. The intraembryonic coelom communicates transiently with the extraembryonic coelom.
  • neuralation - The general term used to describe the early formation of the nervous system. It is often used to describe the early events of differentiation of the central ectoderm region to form the neural plate, then neural groove, then neural tube. The nervous system includes the central nervous system (brain and spinal cord) from the neural tube and the peripheral nervous system (peripheral sensory and sympathetic ganglia) from neural crest. In humans, early neuralation begins in week 3 and continues through week 4.
  • neural crest - region of cells at the edge of the neural plate that migrates throughout the embryo and contributes to many different tissues. In the gastrointestinal tract it contributes mainly the enteric nervous system within the wall of the gut responsible for peristalsis and secretion.
  • pharynx - uppermost end of gastrointestinal and respiratory tract, in the embryo beginning at the buccopharyngeal membrane and forms a major arched cavity within the phrayngeal arches.
  • somitogenesis The process of segmentation of the paraxial mesoderm within the trilaminar embryo body to form pairs of somites, or balls of mesoderm. A somite is added either side of the notochord (axial mesoderm) to form a somite pair. The segmentation does not occur in the head region, and begins cranially (head end) and extends caudally (tailward) adding a somite pair at regular time intervals. The process is sequential and therefore used to stage the age of many different species embryos based upon the number visible somite pairs. In humans, the first somite pair appears at day 20 and adds caudally at 1 somite pair/4 hours (mouse 1 pair/90 min) until on average 44 pairs eventually form.
  • splanchnic mesoderm - Gastrointestinal tract (endoderm) associated mesoderm formed by the separation of the lateral plate mesoderm into two separate components by a cavity, the intraembryonic coelom. Splanchnic mesoderm is the embryonic origin of the gastrointestinal tract connective tissue, smooth muscle, blood vessels and contribute to organ development (pancreas, spleen, liver). The intraembryonic coelom will form the three major body cavities including the space surrounding the gut, the peritoneal cavity. The other half of the lateral plate mesoderm (somatic mesoderm) is associated with the ectoderm of the body wall.
  • stomodeum - (stomadeum, stomatodeum) A ventral surface depression on the early embryo head surrounding the buccopharyngeal membrane, which lies at the floor of this depression. This surface depression lies between the maxillary and mandibular components of the first pharyngeal arch.

System Links: Introduction | Cardiovascular | Coelomic Cavity | Endocrine | Gastrointestinal Tract | Genital | Head | Immune | Integumentary | Musculoskeletal | Neural | Neural Crest | Placenta | Renal | Respiratory | Sensory | Birth

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Cite this page: Hill, M.A. (2015) Embryology Gastrointestinal Tract Development. Retrieved December 1, 2015, from

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