MOLMOL: a program for display and analysis of macromolecular structures.

Current neural induction protocols for human embryonic stem (hES) cells rely on embryoid body formation, stromal feeder co-culture or selective survival conditions. Each strategy has considerable drawbacks, such as poorly defined culture conditions, protracted differentiation and low yield. Here we report that the synergistic action of two inhibitors of SMAD signaling, Noggin and SB431542, is sufficient to induce rapid and complete neural conversion of >80% of hES cells under adherent culture conditions. Temporal fate analysis reveals the appearance of a transient FGF5(+) epiblast-like stage followed by PAX6(+) neural cells competent to form rosettes. Initial cell density determines the ratio of central nervous system and neural crest progeny. Directed differentiation of human induced pluripotent stem (hiPS) cells into midbrain dopamine and spinal motoneurons confirms the robustness and general applicability of the induction protocol. Noggin/SB431542-based neural induction should facilitate the use of hES and hiPS cells in regenerative medicine and disease modeling and obviate the need for protocols based on stromal feeders or embryoid bodies.

/pdf/highly-efficient-neural-conversion-of-human-es-and-ips-cells-5ewq762oqw.pdf

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

I. the origin of species by means of natural selection

https://www.cs.duke.edu/brd/Teaching/Bio/asmb/Papers/NMR/NOE-auto-assignments/Dyana01.pdf

Torsion angle dynamics for nmr structure calculation with the new program dyana

https://www.cell.com/cell/pdf/0092-8674(92)90471-N.pdf

Homeobox genes and axial patterning

A repetitive DNA sequence has been identified in the Drosophila melanogaster genome that appears to be localized specifically within genes of the bithorax and Antennapedia complexes that are required for correct segmental development. Initially identified in cloned copies of the genes Antennapedia, Ultrabithorax and fushi tarazu, the sequence is also contained within two other DNA clones that have characteristics strongly suggesting that they derive from other homoeotic genes.

A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes

The body plan of Drosophila is determined to a large extent by homeotic genes, which specify the identity and spatial arrangement of the body segments. Homeotic genes share a characteristic DNA segment, the homeo box, which encodes a defined domain of the homeotic proteins. The homeo domain seems to mediate the binding to specific DNA sequences, whereby the homeotic proteins exert a gene regulatory function. By isolating the normal Antennapedia gene, fusing its protein-coding sequences to an inducible promoter, and reintroducing this fusion gene into the germline of flies, it has been possible to transform head structures into thoracic structures and to alter the body plan in a predicted way. Sequence homologies suggest that similar genetic mechanisms may control development in higher organisms.

https://science.sciencemag.org/content/sci/236/4806/1245.full.pdf

Homeo boxes in the study of development

Homeodomain-DNA recognition

Pax 6: mastering eye morphogenesis and eye evolution

Pax-6 is a member of the Pax gene class and encodes a protein containing a paired domain and a homeodomain. The molecular characterization of Pax-6 genes from species of different animal phyla and the analysis of Pax-6 function in the developing eyes and central nervous system of vertebrates, Drosophila melanogaster, and Caenorhabditis elegans suggest that Pax-6 homologues share conserved functions. In this review, we present recent data on the structural and functional characterization of Pax-6 homologues from species of different animal phyla. We discuss the implications of these findings for our understanding of the development and evolution of eyes and nervous systems.

https://web.stanford.edu/class/cs379c/archive/2012/suggested_reading_list/supplements/documents/CallaertsetalARN-97.pdf

Walter J. Gehring

Papers

A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes

Homeo boxes in the study of development

Homeodomain-DNA recognition

Pax 6: mastering eye morphogenesis and eye evolution

Pax-6 in development and evolution