User:Henry Savory/sandbox

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Article:[edit]

NOTE: THIS IS THE OLD ARTICLE, I HAVE ALREADY ADDED MY CHANGES TO THE WIKIPEDIA DOCUMENT

Ultrabithorax or Ubx is a gene found in insects, a member of the homeobox gene family, and as many homeobox genes do, functions as a transcription factor. In Drosophila melanogaster it is expressed in the third thoracic (T3) and first abdominal (A1) segments and represses wing formation. The Ubx gene regulates the decisions regarding the number of wings and legs the adult flies will have. Ubx is activated when there is a certain lack of Hunchback (hb) protein. Significant concentrations of Hunchback only exist in the anterior and posterior regions of the embryo, therefore Ubx is expressed only in middle segments. Thus, the hb gene may play an important role in the specification of the boundaries of Ubx expression.[1]

The Ubx gene contains a 5' exon, two micro-exons, an optional B element, and a C terminal exon. The Ubx genomic DNA length is 76 kb and its cDNA clone length is 3.2 to 4.6 kb. The 5' exon contains the 5'UTR which has 964 bases. The C terminal exon contains the 3'UTR which has 1580 to 2212 bases.

The developmental role of Ubx is determined by the splicing that takes place during development. Certain splice factors of a particular cell allow that cell to regulate the developmental fate of that cell by making different splice variants of transcription factors. In D. melanogaster, at least six different isoforms of Ubx exist.[2]

Mutations of the Ubx gene will lead to transformation of dorsal and ventral appendages of the third thoracic segment(T3), which includes the haltere and third leg, into the counterparts on the second thoracic segment(T2). If Ubx is present in T3, it will prevent the original fate of the T2 segment. Such mutations can produce a second set of wings.

Target genes[edit]

Ubx targets hundreds of different genes at different stages of morphogenesis including regulatory genes such as transcription factors, signalling components and terminal differentiation genes.[3]

Ubx represses selected Dpp target genes in the anterior and posterior axis.[4] Ubx represses Wingless in the posterior compartment of the dorsoventral axis. Ubx also selectively represses one enhancer of the vestigial genes in the proximodistal axis.

Regulation[edit]

Expression of Ubx is repressed by the long non-coding RNA Bxd.[5][6]

Ubx Biomaterials[edit]

Besides being a well known transcription factor, Ubx has been used to form biomaterials in vitro. Macroscale materials in the form of ropes, films and sheets can be generated from recombinant Ubx protein, which can self-assemble under gentler conditions than other biomaterial proteins.[7] The macroscale materials self-adhere, allowing them to assume more complex structures. In addition to requiring less harsh conditions than other proteins, Ubx has been shown to assemble more rapidly and at much lower concentrations.[7]

Ubx materials are mechanically robust. By altering fiber diameter, the breaking strength, breaking strain, and Young’s modulus can be tuned to values spanning an order of magnitude, ultimately changing the mechanism of extension.[8]

References[edit]

  1. ^ White RA, Lehmann R (October 1986). "A gap gene, hunchback, regulates the spatial expression of Ultrabithorax". Cell. 47 (2): 311–321. doi:10.1016/0092-8674(86)90453-8. PMID 2876779.
  2. ^ "FlyBase Gene Report: Dmel\Ubx". FlyBase. March 20, 2009. Retrieved 2009-04-23.
  3. ^ Pavlopoulos A, Akam M (2011). "Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis". Proc Natl Acad Sci U S A. 108 (7): 2855–2860. doi:10.1073/pnas.1015077108. PMC 3041078. PMID 21282633.
  4. ^ Capovilla M, Brandt M, Botas J (February 1994). "Direct regulation of decapentaplegic by Ultrabithorax and its role in Drosophila midgut morphogenesis". Cell. 76 (3): 461–475. doi:10.1016/0092-8674(94)90111-2. PMID 7906203.
  5. ^ Petruk S, Sedkov Y, Riley KM, et al. (December 2006). "Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference". Cell. 127 (6): 1209–21. doi:10.1016/j.cell.2006.10.039. PMC 1866366. PMID 17174895.
  6. ^ Petruk S, Sedkov Y, Brock HW, Mazo A (2007). "A model for initiation of mosaic HOX gene expression patterns by non-coding RNAs in early embryos". RNA Biol. 4 (1): 1–6. doi:10.4161/rna.4.1.4300. PMID 17568198.
  7. ^ a b Greer AM, Huang Z, Oriakhi A, Lu Y, Lou J, Matthews KS, Bondos SE (2009). "The Drosophila transcription factor ultrabithorax self-assembles into protein-based biomaterials with multiple morphologies". Biomacromolecules. 10 (4): 829–837. doi:10.1021/bm801315v. PMID 19296655.
  8. ^ Huang, Z.; Lu, Y.; Majithia, R.; Shah, J.; Meissner, K.; Matthews, K. S.; Bondos, S. E.; Lou, J. (2010). "Size Dictates Mechanical Properties for Fibers Self-Assembled by the Drosophila Hox Transcription Factor Ultrabithorax". Biomacromolecules. 11 (12): 3644–3651. doi:10.1021/bm1010992. PMID 21047055.

External links[edit]

Peer Reviews:[edit]

Stephanie Porche – Epimorphosis[edit]

The revision of the introduction and addition of the history section made the article much more informative, so we get a better understanding of epimorphosis and its implications in biology. The subject of scientific implications could have been expanded upon, to discuss if there is any use for this information beyond understanding the concept. Both illustrations work well to support the information, however the image of newt limb regeneration is way below the actual information and would work better further up (if possible). All the information seems well referenced, and the article has definitely been improved.

Roma Ballena Palomino – Invagination[edit]

There is a clear description of cell movements which occur during invagination in tunicates and amphioxus, however there are a few improvements which could be made. A short description of the species would be appropriate (e.g. what amphioxus/lancelets are and how they are biologically classified), and a picture of invagination in tunicates would also help. There are multiple relevant references, though there could be more citations in the paragraph body – cite specific information. The Biology and Humanities sections are a little unclear, even though they contain relevant information. Maybe the Biology section should come before the specific examples (tunicates etc.), and the importance of the Humanities section could be explained more.

Konur Oyman – Deep Homology[edit]

I cannot specifically find the work that Konur has done, all recent edits (January and March 2018) seem to come from another editor and there are no edits in his sandbox. From what is present in the Wikipedia article, I think that the Introduction and History sections are clear and concise and get the reader familiar with the concept. The information in the second section is relevant and well referenced, however it might be easier to read if there were subsections to make each concept clearer. Both illustrations are well described and support the information in the body of the article.

Work[edit]

Ultrabithorax (Ubx)
Figure 1- Homeobox gene of Drosophila Melanogaster

Ultrabithorax or Ubx is a gene found in insects, a member of the homeobox gene family, and as many homeobox genes do, functions as a transcription factor. In Drosophila melanogaster it is expressed in the third thoracic (T3) and first abdominal (A1) segments and represses wing formation. The Ubx gene regulates the decisions regarding the number of wings and legs the adult flies will have. Ubx is activated when there is a certain lack of Hunchback (hb) protein. Significant concentrations of Hunchback only exist in the anterior and posterior regions of the embryo, therefore Ubx is expressed only in middle segments. Thus, the hb gene may play an important role in the specification of the boundaries of Ubx expression.[1]

The Ubx gene contains a 5' exon, two micro-exons, an optional B element, and a C terminal exon. The Ubx genomic DNA length is 76 kb and its cDNA clone length is 3.2 to 4.6 kb. The 5' exon contains the 5'UTR which has 964 bases. The C terminal exon contains the 3'UTR which has 1580 to 2212 bases.

The developmental role of Ubx is determined by the splicing that takes place during development. Certain splice factors of a particular cell allow that cell to regulate the developmental fate of that cell by making different splice variants of transcription factors. In D. melanogaster, at least six different isoforms of Ubx exist.[2]

Mutations of the Ubx gene will lead to transformation of dorsal and ventral appendages of the third thoracic segment(T3), which includes the haltere and third leg, into the counterparts on the second thoracic segment(T2). If Ubx is present in T3, it will prevent the original fate of the T2 segment. Such mutations can produce a second set of wings.

Target genes[edit]

Ubx targets hundreds of different genes at different stages of morphogenesis including regulatory genes such as transcription factors, signalling components and terminal differentiation genes.[3]

Ubx represses selected Dpp target genes in the anterior and posterior axis.[4] Ubx represses Wingless in the posterior compartment of the dorsoventral axis. Ubx also selectively represses one enhancer of the vestigial genes in the proximodistal axis.

Regulation[edit]

Expression of Ubx is repressed by the long non-coding RNA Bxd.[5][6]

Ubx Biomaterials[edit]

Besides being a well known transcription factor, Ubx has been used to form biomaterials in vitro. Macroscale materials in the form of ropes, films and sheets can be generated from recombinant Ubx protein, which can self-assemble under gentler conditions than other biomaterial proteins.[7] The macroscale materials self-adhere, allowing them to assume more complex structures. In addition to requiring less harsh conditions than other proteins, Ubx has been shown to assemble more rapidly and at much lower concentrations.[7]

Ubx materials are mechanically robust. By altering fiber diameter, the breaking strength, breaking strain, and Young’s modulus can be tuned to values spanning an order of magnitude, ultimately changing the mechanism of extension.[8]

References[edit]

  1. ^ White RA, Lehmann R (October 1986). "A gap gene, hunchback, regulates the spatial expression of Ultrabithorax". Cell. 47 (2): 311–321. doi:10.1016/0092-8674(86)90453-8. PMID 2876779.
  2. ^ "FlyBase Gene Report: Dmel\Ubx". FlyBase. March 20, 2009. Retrieved 2009-04-23.
  3. ^ Pavlopoulos A, Akam M (2011). "Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis". Proc Natl Acad Sci U S A. 108 (7): 2855–2860. doi:10.1073/pnas.1015077108. PMC 3041078. PMID 21282633.
  4. ^ Capovilla M, Brandt M, Botas J (February 1994). "Direct regulation of decapentaplegic by Ultrabithorax and its role in Drosophila midgut morphogenesis". Cell. 76 (3): 461–475. doi:10.1016/0092-8674(94)90111-2. PMID 7906203.
  5. ^ Petruk S, Sedkov Y, Riley KM, et al. (December 2006). "Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference". Cell. 127 (6): 1209–21. doi:10.1016/j.cell.2006.10.039. PMC 1866366. PMID 17174895.
  6. ^ Petruk S, Sedkov Y, Brock HW, Mazo A (2007). "A model for initiation of mosaic HOX gene expression patterns by non-coding RNAs in early embryos". RNA Biol. 4 (1): 1–6. doi:10.4161/rna.4.1.4300. PMID 17568198.
  7. ^ a b Greer AM, Huang Z, Oriakhi A, Lu Y, Lou J, Matthews KS, Bondos SE (2009). "The Drosophila transcription factor ultrabithorax self-assembles into protein-based biomaterials with multiple morphologies". Biomacromolecules. 10 (4): 829–837. doi:10.1021/bm801315v. PMID 19296655.
  8. ^ Huang, Z.; Lu, Y.; Majithia, R.; Shah, J.; Meissner, K.; Matthews, K. S.; Bondos, S. E.; Lou, J. (2010). "Size Dictates Mechanical Properties for Fibers Self-Assembled by the Drosophila Hox Transcription Factor Ultrabithorax". Biomacromolecules. 11 (12): 3644–3651. doi:10.1021/bm1010992. PMID 21047055.

External links[edit]

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