Websites of note

Donald Ingber (Yale graduate) is the Founding Director of the Wyss Institute for Biologically Inspired Engineering at Harvard University. He is also Professor of Vascular Biology at Harvard Medical School and Boston Children's Hospital and Professor of Bioengineering at the Harvard School of Engineering and Applied Sciences. He is an outstanding public speaker (try viewing www.youtube.com/watch?v=z2mK3-tV08I) and I was fortunate to hear him give a talk on his special subject of organs on a chip. Briefly, this means creating a fabric of cells in vitro that mimic in vivo conditions with much greater fidelity than free cultured cells. Ingber has identified the mechanisms that living organisms use to self-assemble cells to create functional organs. This has led to a biomimetic platform in which microfabrication techniques from the computer industry are used to build functional circuits with living cells as components. The result is organs on chips that mimic complicated human functions. The chips can replace traditional animal-based methods for testing drugs and for creating human disease models. Ingber recognized that cells exhibit tensegrity architecture, first described by Buckminster Fuller for structures that achieve integrity only when in tension. This structure explains how living cells are structured to respond biochemically to mechanical forces. In looking at the control of angiogenesis and vascular development, the process of functional tissue construction has been found to be regulated mechanically. Living cells stabilize their internal cytoskeleton and control their shape via integrin receptors initiating cellular rebuilding. The extracellular matrix and change of cell shape not only play central roles in normal function, but also in angiogenesis that allows tumor growth and expansion. The website given here has basic information and links to research publications. Although the site has apparently not been updated since 2011, it provides the basics of organs on a chip before searching for more recent literature. Ingber has received the Holst Medal, Pritzker Award from the Biomedical Engineering Society and many other accolades. He epitomizes a successful scientific career and is a worthy role model for students. As Ingber said, come to this website and you will see the future. NASA's Offshore Membrane Enclosures for Growing Algae (OMEGA) is a major development project using selected algae to clean wastewater, to capture carbon dioxide, and to produce biofuel (Fig. 1). This is intended to complement agricultural production by using runoff waste and sewage so that biomass production does not compete with agriculture for water, fertilizer, or land. Large flexible plastic tubes (photobioreactors) can float in seawater or sewage dams. The algae are selected for rapid growth producing biomass that can be converted into biofuels, fertilizer, and animal food. The algae remove nutrients that would otherwise contribute to aquatic dead-zone formation. Demonstrations have shown promise on a small scale. Jonathan Trent presents a clear exposition of the potential in a talk titled “Energy from floating algae pods” (www.youtube.com/watch?v=X-HE4Hfa-OY). Such projects will employ many of our biochemistry graduates, but as Jonathan Trent says “It is not going to be easy.” I have used this project to add interest and relevance to lectures on photosynthesis and other topics overlap with the principles of the OMEGA system. NASA's Offshore Membrane Enclosures for Growing Algae (OMEGA) has been demonstrated to work in San Francisco bay. Hopefully, it will become a commercial application and provide employment for our graduates. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.] The Institute of Education Sciences was created in the US by the Education Sciences Reform Act of 2002 as the research arm of the Department of Education. It is the successor to the Office of Educational Research and Improvement. The institute is divided into four major research and statistics centers: (1) The National Center for Education Statistics that conducts the National Assessment of Educational Progress known as The Nation's Report Card, (2) The National Center for Education Research, (3) The National Center for Education Evaluation and Regional Assistance that operates the National Library of Education and the Education Resources Information Center and (4) The National Center for Special Education Research. The institute activities are aimed at identifying best practice, a rather different emphasis to much of the literature on education. The institute has conducted randomized controlled trials in schools to find out whether some textbooks are better than others and whether professional development programs for teachers improve student achievement. It has conducted extensive research to assess compliance with the No Child Left Behind Act of 2001. Although K-12 level education is a major focus, tertiary teaching is also covered and topics of interest can be located using the search box at the site. The What Works Clearinghouse (http://ies.ed.gov/ncee/wwc/) is an institute service with 10,310 research papers available to answer questions such as how to reduce dropout rates or help students with special needs. Under What's New for August 2014 the results of a study titled “Interactive Online Learning on Campus: Testing MOOCs and Other Platforms in Hybrid Formats in the University System of Maryland” reveals that students in hybrid courses and students in traditional courses performed equally well in terms of course pass rates and grades. The study authors further reported that they found no evidence that interactive online learning was harmful for disadvantaged or underprepared students. This site has an educational resources section with a number of simple screens of information about the health benefits of high fiber diets based on grains. I have adapted some of this information to include with lectures on nutrition. Not surprisingly the site extolls the virtues of whole grain foods for weight loss and reduced incidence of common diseases. The material adheres to a sound evidence base and there are fact sheets and brochures to download. An interesting table is located under the section on legumes that lists the cost per gram of protein in foods showing peas and lentils as the best value. The legumes are additionally promoted as good sources of iron, essential fatty acids, soluble and insoluble fibre and micronutrients. The recipes given here may even stimulate you to do some experimental work in the kitchen. This is a short site from the University of Western Australia, but should stimulate thinking about biochemistry and its explanation of life processes. After reading through the questions posed here you might easily think of ten more interesting questions to pose. Some of the answers that are given could be a source of long debate about their inclusiveness and could stimulate some good discussion in a flipped classroom. The questions are as follows. What does DNA do? If you stretched out your entire DNA from just one cell, how long would it be? Why aren't identical twins really identical? What's in egg white that makes it turn hard when boiled? Why are leaves green? Why is breast milk best for babies? What takes the oxygen from your lungs to cells in your body? What is the most abundant protein in the world? Which parts of the glucose molecule do you think the cell can access for energy? How many of these C-C + C-H bonds are actually required by a human? How much energy in a molecule of glucose can a cell actually access? How much energy to do you need to climb Bluff Knoll (a local peak)? I climbed Bluff Knoll as a young man and my answer to the last question was more qualitative than the answer they work through. Wiley publishers provide this website as a companion to Rodney Boyer's text Concepts in Biochemistry. It provides a refresher (or introduction) to basic chemistry that is often assumed knowledge before taking biochemistry classes. The topics covered are elementary kinetics, logarithms, pH and buffers, redox reactions and thermodynamics. Boyer is a long time contributor to this journal and has a fluency honed over many years of writing texts and learning from his teaching experiences. The information here is succinct, accurate and colorful. If you are tired of recapitulating this material then send your students to this site. While you are at the site check the interactive animations which are reasonably comprehensive across most aspects of biochemistry. They are a bit simplistic, but make good summaries of major pathways. For small molecule interactions with proteins CREDO is a relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small molecules and the macromolecules found in structures in the Protein Data Bank (PDB). The website is commendably graphic with easy introductions and could be adapted for teaching in courses that perform structure modelling and data base interrogation. This website was promoted by Sir Thomas Blundell at the 2014 FAOBMB conference in Taiwan. Blundell's research has revealed many structural associations using methods from biochemistry, protein crystallography, bioinformatics and structure-based drug design. Systems studied by Blundell include DNA repair, hormones and growth factors, cellular signaling, crystallins, renin and HIV protease. His group has written several bioinformatics programs in addition to CREDO. Blundell's research began with training in the lab of Dorothy Crowfoot-Hodgkin. His biography is in Wikipedia and is a life fully lived in academia, business and politics. Blundell's life is a remarkable role model for students and the more remarkable for the creation of a billion dollar company. Blundell has a stellar grasp of the mechanisms of protein-protein interactions, one to one and in aggregate complexes. The home page has latest publications featuring ultrastructure never seen before. The National Center for Microscopy is not only a unit that uses microscopes, it also generates advances and refinements for all microscopy techniques. To paraphrase the words of Mark Ellisman from the Center talking at the 2014 FAOBMB conference in Taiwan, “We take the best others can do and make it better.” The sequence of slides and movies he showed to reveal three-dimensional cellular structure was spectacular. He pointed out how textbooks overly simplify structure. When real cells are imaged, it is apparent how cells are densely packed with organelles, so much so that cytosol is a minor feature. Endoplasmic reticulum is far more dense in liver cells than most would believe. The home page features research highlights with highly engaging topics and images that make for excellent browsing. For a quick visual start, select the gallery option from the top menu. One article featured in October 2014 is Electron Microscopy Achieves a New APEX. This article describes how Ellisman and others designed a GFP equivalent for electron microscopy. This tag, unlike conventional stains, provides specific visualization of tagged proteins with much higher resolution than fluorescence microscopy. The new tag has been used to highlight proteins located in mitochondria, nuclei, endoplasmic reticulum and cytosol. The Enzyme Function Initiative (EFI) provides predictions of enzymatic and physiological functions of unknown enzymes discovered in genome projects. This is accomplished by integrating bioinformatics, structural biology, enzymology, genetics, and metabolomics. The TrEMBL database contains the translations of all coding sequences present in the EMBL/GenBank/DDBJ Nucleotide Sequence Databases and also protein sequences extracted from the literature or submitted to UniProtKB/Swiss-Prot. Fifty percent of the sequences in the database have uncertain functions and these can be analyzed by the EFI. The EFI is formed from 80 researchers at nine academic institutions in the United States and Canada. Two of the tools available at the site are the Enzyme Similarity Tool and the Genome Neighborhood Tool. The outputs from these programs are cluster diagrams that can be refined by entering various degrees of stringency to matches. The tools have tutorials to teach users how to begin. Unknown genes and proteins can accordingly be assigned probable functions using activity data that takes the analysis far beyond sequence homology. Look under publications for some well-illustrated papers showing predicted enzyme actions and affinity linkages. Every lecturer, veteran or new, should read this article because it is explicit about what not to do. It also tells you how to win an audience with high-impact approaches. Some gems in the article include the following. We all know that humans are wired to listen to stories. Metaphors and narrative structures work best to engage people. A successful talk is a little miracle—people see the world differently afterward. Also pay attention to your tone. Some speakers may want to come across as authoritative or wise or powerful or passionate, but it's usually much better to just sound conversational. Don't force it. Don't orate. Just be you. The biggest mistake we see is that people move their bodies too much. They sway from side to side, or shift their weight from one leg to the other. People do this naturally when they're nervous, but it's distracting and makes the speaker seem weak. Simply getting a person to keep his or her lower body motionless can dramatically improve stage presence. There are some people who are able to walk around a stage during a presentation, and that's fine if it comes naturally. But the vast majority are better off standing still and relying on hand gestures for emphasis. Perhaps the most important physical act onstage is making eye contact. The URL given here begins with a lower case “L” (in case it is ambiguous). The parent publication for this article is the Harvard Business Review. Not surprisingly most of the articles at the hbr.org site relate to business and leadership. Educational Institutes have become business environments so it is likely that if you browse the hbr.org site that you will find numerous articles of interest among the free articles.

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