Websites of note

Abstract

The following passage from the Proteopedia site looks like conventional textbook information on hemoglobin except that the phrases printed in italics cause the displayed model of hemoglobin (Fig. 1) to zoom to the selected feature. “Hemoglobin is an allosteric protein. It is a tetramer composed of two types of subunits designated α and β, with stoichiometry α2β2. The four subunits of hemoglobin sit roughly at the corners of a tetrahedron, facing each other across a cavity at the center of the molecule. Each of the subunits contains a heme prosthetic group. The heme molecules give hemoglobin its red color. Each individual heme molecule contains one Fe2+ atom. In the lungs, where oxygen is abundant, an elemental oxygen molecule binds to the ferrous iron atom of the heme molecule and is later released in tissues needing oxygen. The heme group binds oxygen while still attached to the hemoglobin monomer. The space filling view of the hemoglobin polypeptide subunit with an oxygenated heme group shows how the oxygenated heme group is held within the polypeptide. Anchoring of the heme is facilitated by a histidine nitrogen that binds to the iron.” It does not get any better than this for convenience in interacting with protein models. The choices to manipulate the model are presented in green, with the more familiar hyperlinks to other text and definitions presented in blue. The look and feel of the site is identical to Wikipedia, and although the site is a wiki (you can add and modify), it is not Wikipedia. I was disappointed to find that aspartate transcarbamoylase was absent from the extensive list of 55,240 articles, but Protopedia allows for custom creation of tutorials without the need to learn any scripting language. Eric Martz, a founder of molecular modeling approaches for personal computers, has made many of the entries by importing from his established database. The Proteopedia site is unhelpful in providing the story of the establishment of the site, but fortunately, this background is in an online article at genomebiology.com/2008/9/8/R121. I am grateful to Judy Voet for bringing this site to my attention. I will be commending this site to my students and may even use it directly in lectures. The site is far from mature, but it is a definite must visit. Hemoglobin, as rendered by the JMol modeling utility used in Proteopedia. The user can interactively change the view and the details displayed. URLs (Web addresses) can be ridiculously long with lots of slashes separating the host domain from subsidiary servers and folders. The tinyurl utility available from this site takes the long name of a URL and stores that long name at the tinyurl site as a short pointer. For example tinyurl.com/6p9gzw will turn into http://www.macworld.com/article/134608/2008/07/portableapplications.html?lsrc=rss_main. This example came to me from a newspaper article that quoted numerous Web pages referenced by tinyurl URLs. This made for much easier reading of the article, even though information was lost. When students see a long URL on a slide or handout it is unlikely that they will bother to follow up on those long URLs when they must enter them manually. You can give them both URLs so they know where they will be directed. Tinyurl is a brilliant application. The 1000 Genomes Project will develop a map of the human genome that will catalogue DNA variations. This is intended to illuminate the nature of genetic diseases and provide an analysis of population clusters. A set of guidelines outlining ethical considerations requires that genomes contributed are submitted only after completion of an informed consent form. Final decisions about which populations, and which sample sets, will be included in the project will be made by a steering committee. Inherent in the name is that the project will catalogue the genomes of at least a 1,000 people from around the world. Funding has been offered by the Wellcome Trust Sanger Institute UK, the Beijing Genomics Institute, and the National Human Genome Research Institute, part of the National Institutes of Health. The primary contact for the project is Richard Durbin, from the Wellcome Trust Sanger Institute. A 3-year timeline is anticipated for completion of the project, and data will be made freely available for research. The Society for General Microbiology was founded in 1945 and is the largest microbiological society in Europe. It has over 5,000 members with 75% residents in the UK. The membership comes from universities, research institutes, health services, and corporations. This large and diverse membership supports a full time management staff of 30 people who offer many services, including regularly updated summaries of news and developments in microbiology. The staff is located at Marlborough House, Reading, UK. The society produces four issues per year of the magazine Microbiology Today. This magazine has a theme for each issue, and the six most recent themes have been life is a gas, life on us, bugs get everywhere, microbes shaping history, actinobacteria, and food and water. In this issue with the theme life is a gas, I was able to download pdf files of the articles (eight articles in the issue). The lead article Microbes and oxygen relates that the oxygen in our atmosphere began as a waste product. Microbes also make oxygen, not only higher plants. Probably, half of the oxygen produced per year comes from the oceans, and half of this is derived from cyanobacteria of which half are infected by viruses at any one time. The interesting effect of these viruses on enhancing oxygen production (and energy production) in cyanobacteria is described in the article. The Brutlag Bioinformatics Group is located in the Biochemistry Department at Stanford University. The site allows for download of several computer programs for cutting edge analysis of the projected structure and function of proteins that can be predicted as products of a given DNA segment. This is the field known as functional genomics. The group is interested in predicting the location of promoters and other DNA regulatory sequences, small molecule and protein docking sites, identifying drug targets, and drug design. The group has found novel ways of discovering transcription factor binding sites and finding conserved DNA consensus sequences as short as eight base pairs. The group offers courses in computational molecular biology, bioinformatics, genomics, and proteomics. Some of the courses are available online via the Stanford Center for professional development. The courses are primarily aimed at practicing scientists and include the award of formal qualifications on completion. I still get a daily delivery of a print newspaper, but this is not the way the net-savvy generation is getting information. The wasteful depredation of forests may provide the ultimate motivation to move to virtual ways of acquiring transient general information. There are several utilities in addition to Feedreader that belong to a generic group dubbed RSS services. The initials RSS are used to refer to: really simple syndication, RDF site summary, or rich site summary. What you get is a utility that constantly monitors updates to news sites that you select and provides an easy entry to that topical information. The Feedreader Web site shows screen shots of typical usage and illustrates how users can additionally acquire commercial and descriptive information on products such as cars. The categories of updates can be arranged into folders. An RSS service can look at blogs of interest and let you know when something new has been added. Scientific journals could also be incorporated into an RSS service. The Wikipedia article on RSS services provides a history of this category of software and relates how pioneering programs, dating from 1995, did not become popular until recent years. The promotional information from Feedreader proclaims “Feedreader offers the broadest range of capabilities, and provides advanced, state-of-the-art features that cannot be found in any other aggregation solution. Its unique smart feed capability helps users immediately find the information that is most important and relevant to them. Users create smart feeds by simply entering key words or phrases that relate to their topic of interest. Feedreader then automatically monitors articles for those topics, and displays them in the left feed panel. Best of all, it is free.” By serendipity, I checked my e-mail after assembling the above information and found that my son's RSS service had told him that the local trains have just been cancelled so he passed the information on, knowing that I was not using an RSS service. This is the way of the future. This magazine is provided by the company CambridgeSoft that markets the ChemDraw suite of products. The magazine has both print and online versions and claims to be in use by 400,000 scientists worldwide. There is a dedicated and extensive user group that has developed around the ChemDraw suite of programs in both education and industry. This issue at the time of review featured an article by Sheryl Baldwin titled “Enhancing Innovative Undergraduate Science Education Programs at Virginia Commonwealth University with ChemBioDraw Ultra.” Another article was on the product ChemFinder, a database that stores chemical structures, physical properties, notes and tables of data. You can subscribe to either the electronic or print form of the newsletter, at no cost, by registering at the Web site. ALT is a professional and scholarly association based in the UK with a full time administration staff. The annual ALT conferences are important international meetings for everyone involved in multimedia applications. ALT defines learning technology as the broad range of communication, information and related technologies that can be used to support learning, teaching, and assessment. This is a broad segment of all tertiary teachers and, as they claim, you do not have to call yourself a learning technologist to be one and benefit from ALT activities. Look in the documents folder on the Website to locate a list of papers on policy and practice in learning technologies. The proceedings of association conferences (called ALT-C) also give interesting information. ALT-C for 2008 was held in Leeds and titled Rethinking the digital divide. ALT-C 2009, scheduled for Manchester in September, is titled In dreams begins responsibility: choices, evidence, and change. Mary Harrsch is at the University of Oregon and claims to be passionate about technology, education, and history, particularly ancient history. These interests have combined to produce a well illustrated and engagingly presented compilation of medical riddles through time. Did you know that Shakespeare's portraits point to Mikulicz Syndrome and systemic sarcoidosis? The author puts it best herself in her introduction, which is quoted next. “Did Agrippina poison the Roman Emperor Claudius? Was General George Armstrong Custer mentally sound when he ordered the seventh Cavalry to attack at the Little Big Horn River? History is full of medical mysteries. After all, everyone has to die of something. But modern medical practitioners have actually found clues to the progress of diseases that still afflict mankind today by studying ancient sources who recorded the afflictions and demise of peoples of the past. Each year, at a clinicopathological conference sponsored in part by the U.S. Department of Veterans Affairs and VA Maryland Health Care System in conjunction with the University of Maryland School of Medicine, a panel of physicians led by Dr. Philip A. Mackowiak analyze the medical history of a famous person of the past. Using modern forensic science, they propose modern diagnoses for the individual and speculate on the effectiveness of medical procedures used by physicians of the period. Some of these cases (and more) are examined here.”