21 st Century Biology

1. Experimental Biology for Pre-College Students: An Introduction to Modern Research Techniques and Scientific Writing 21st Century Biology www.21bio.org

2. Volume 2-Issue 1 September-October 2002 Brainstorm Alcohol: All Kinds of Bad and, in quantities large enough to be toxic, death”. Understanding how alcohol creates this eclectic spectrum of effects in people has always been difficult for scientists. Alcohol is a great solvent (it can dissolve things easily): fats dissolve particularly well. Because cell membranes in the brain are made of lipids (Fatty compounds), alcohol can seep into brain cells. However alcohol just being in the cells does not create its effects. Most recreational drugs effect people by binding to nerve receptors, and preventing the normal function of nerve transmitters and the nervous system as a whole. Alcohol however, does not have its own nerve receptor to bind to, as do drugs like heroine and cocaine. Scientists now believe that alcohol can bind to a wide variety of nerve receptors. Because alcohol can affect different kinds of nerve receptors, it can create many different reactions. Alcohol is an addictive substance. Addicted people are said to have “alcoholism”. Scientists continue to try to understand alcohol on the molecular level to try to create a drug to treat people with alcoholism. Resources: www.dana.org/articles/dbk_0298.cfm - 18k - 25 Sep 2002 Alcohol is one of the world’s oldest drugs. Ethyl alcohol is the common alcohol found in beverages, it is abundant because it is a byproduct of yeast’s cellular respiration. When people consume large amounts of alcohol it affects the brain and can cause varied reactions: “First comes a "high," then, with larger amounts, sedation, unconsciousness, Editors: Annie Lagomarcino Addie Leader-Zavos Reid Ravin Try to find your way through this fun maze! Sidwell Friends School Inside this issue: Thigmomorphogenesis 2 Brain Awareness Week 2 Zebrafish 3 Telemicroscopy 3 Chesapeake Bay Foundation 4 Wordfind 4

3. Brain Awareness Week A Brain A Basic Neuron

4. The Neurophysiology, Behavior, and Bioacoustics of Insects

5. Immunocytochemistry in Conjunction with the NIH

6. Weakly Electric Fish (WEF) The sound that you are hearing is a “clicker” that is eating • The picture on the right shows a graph of the field of an electric fish. Note that the field is strongest near the tail and rapidly weakens as the distance from the fish increases. This gives a fairly accurate sense of distance, if not an exact shape impression.

7. WEF Applications • Military Sensory Applications • Electric Fish as Biosensors • Medical Applications • Non-Contact Human-Computer Interfaces

8. Thigmomorphogenesis Monocots vs. Dicots Arabidopsis RNA Extraction

9. Thigmomorphogenesis Setup

10. Zebrafish • The Zebrafish Project was Started at Sidwell Friends by Biology I Students • Goals • Start a Zebrafish Colony • Investigate Developmental Mutations of Notochords • Write LiCl Treatment Protocols • Focus on Spadetail, Floating Head, and Hedgehog Mutations

11. Genome Duplication Events in Zebrafish Evolution http://www.ittiofauna.org/webmuseum/agnati/ Zebrafish Agnatha Osteichthyes Teleosts Ancestral chordate Vertebrata Pufferfish Chondrichthyes Urochordata http://www.ucmp.berkeley.edu/vertebrates/basalfish/chondrolh.html http://www.cosmiverse.com/science10260102.html Cephalochordata Fig. 2 Genome duplication event

12. With Wnt signal No Wnt signal GSK3ß Wnt P β-catenin Ubiquitin-proteosome system Tcf3 Wnt RNA transcriptase Frizzled Nucleus Hox genes GSK3ß The Wnt signaling pathway • A neighboring cell secretes Wnt to the target cell. • Wnt binds to the target cell’s receptor, frizzled. • Frizzled blocks the GSK3ß complex, which normally phosphorylates ß-catenin. • Unphosphorylated ß-catenin binds to the Tcf3 complex, a transcription repressor in the nucleus. • Inhibiting the Tcf3 complex permits the transcription of Hox genes that regulate AP axis development. β-catenin Tcf3 Key Transcription of Hox genes inhibition

13. The Hox expression gradient and establishment of the AP axis Hox gene cluster anterior-determining genes posterior-determining genes posterior anterior The Hox expression gradient acts like a continuous spectrum of different colors. For example, the embryo’s head is determined by 100% red (the first Hox gene) and 0% other (the other Hox genes). A middle segment would be determined by 50% yellow (a middle Hox gene) and 50% green (the next Hox gene). By this mechanism, Hox regulates normal embryonic differentiation, leading to neurogenesis and organogenesis both along the anterior-posterior (AP) axis and along the dorsal-ventral (DV) axis.

14. The Floating Head Mutant Gastrulation wt flh Cells that have not entered the hypoblast continue to maintain normal flh gene expression. Cells in flh mutants that have involuted and entered the hypoblast show an abrupt loss of flh expression.

15. The Sonic-You (Syu) Gene Sonic-You (syu) gene encodes for sonic hedgehog (shh) protein and is required for somite patterning. The syu mutant is missing the syu Gene and the shh signaling pathway does not function properly, and so what the shh gene encodes cannot be distributed. Shh signaling pathway Smoothened is a protein believed to activate an intracellular signaling cascade. It forms a receptor complex with Patched. Patched is a protein thought to be the receptor that binds the shh gene and induces conformational changes in itself and Smoothened. When Patched represses Smoothened, the shh protein cannot be involved in the organization and patterning of tissues in vertebrates or control a wide range of differentiation processes during vertebrate development, especially floor plate development. Mutations develop when this occurs. Wnt4b is a protein expressed exclusively in the floor plate. If shh is missing, the wnt4b cannot Function properly, so the lateral floor plate is not developed fully, sometimes not at all. Many mutations display these characteristics.

16. The Spadetail Mutant The Spadetail gene encodes for a T-box transcription factor that encodes a message that is expressed in the blastoderm soon after initial zygote gene expression. After gastrulation, its expression is restricted to paraxial mesoderm and later in the developing tail bud. spt Zfin.org Together with another gene, ntl, spadetail mediates the signaling of fibroblast growth factor (FGF). The spadetail mutant does not express the spadetail gene. The t-box gene that corresponds to the spadetail mutants is tbx16. FGF is responsible for trunk and tail Formation. Spadetail is responsible Specifically for FGF signaling in the trunk non-notochordal mesoderm. Without the spadetail gene, mutants have major trunk mesoderm deficiencies, but relatively normal tail and notochord development.

18. Telemicroscopy & Tomography

19. Locations of Microscopes California State University Stanislaus Confocal Microscope IN-VSEE Arizona State University Scanning Probe Microscope National Center for Microscopy and Imaging Research UCSD Transmission Electron Microscope