Websites of note

www.icgc.org Each cancer genome has somatic alterations, designated as driver mutations that cause the cancer to develop. The search for driver mutations has become a central aim of cancer research and more than 300 genes have already been identified. The study of these genes has generated most of our insights into the process of oncogenesis. The practical outcome is that cancer genes and the pathways in which they are involved can be inhibited by therapeutic agents. Passenger mutations, which do not contribute to the neoplastic phenotype, additionally provide a molecular record of each cancer's evolutionary past, reflecting past mutagenic exposures and intrinsic defects of DNA repair. As a result, they can give clues about the etiology of individual cancers. There are major differences among cancer types both in the driver mutations and in the numbers and types of passenger mutations found. Our understanding of patterns of somatic passenger mutation in cancer is at an early stage and there are many cancer genes still to be identified. Establishing a complete catalogue of somatic genetic changes in individual cancers will therefore reveal the full set of driver mutations and cancer genes that are operative in each type of cancer. It will also reveal the full set of passenger mutations and hence yield insights into underlying mutational processes. The International Cancer Genome Consortium aims to rationalize the research and create a compendium of genomic alterations in cancer subtypes. This has not been achieved yet, but the site has links to all of the groups working on specific cancers such as colorectal, breast, and liver. www.bera.ac.uk The Association was formed in 1974 and has a membership largely derived from the academic areas of psychology, sociology, history, and philosophy. Nevertheless the activities of the Association are relevant to all educators interested in curriculum, pedagogy, assessment, and management. The general aim of the association is to better inform decisions about educational outcomes and it does this through conferences and publications. The annual cost of membership is £65 and seems to be good value considering it is a large professional society with a full range of member services. Members receive four copies per annum of the magazine Research Intelligence. Fortunately, the content can be downloaded in pdf format from the publications section of the web site. Issue 110 of the magazine for Spring 2010 includes an article entitled “Measuring impact in education.” This article states that for career advancement in laboratory science the formula of publishing in high impact journals is well established, but high impact journals in education research simply do not exist. This unfortunately includes BAMBED with an annual impact factor hovering around 0.6. One colleague who publishes in the field of education did see a positive side to this and related that most of his articles were in zero-impact publications. The magazine article discussing impact factors in Research Intelligence concludes “our own experience is that many academics in the discipline of Education work in the field largely because they hope their work will have a positive impact for learners in particular and society in general.” While Research Intelligence is the regular magazine, the high prestige publication from the Association is The British Educational Research Journal published by Routledge Taylor & Francis. This journal is indexed by the Institute of Scientific Information and is listed in Current Contents. Abstracts are on the web. My library has an institutional subscription to the journal and you may be similarly able to obtain full text. www.fyhe.com.au The International Journal of the First Year in Higher Education is a new online publication covering research and practice for enhancing the first year in higher education. Over the last decade, my university has keenly increased attention to retention, performance, and happiness of our first year students. The transition between school and university has been fraught with many challenges and individual support at critical times can be the difference between confident progress and losing the way and dropping out. First year classes are often large and impersonal. Few lecturers have the in-born talent to hold and motivate these large classes. So many things have to be right to succeed with first year classes that it is timely to have a new journal dedicated to this phase of study. As more school-leavers progress to higher education, our students have changed in character because they include more who would not have chosen an academic path in earlier times. Also, changing is the technology that new students bring with them which can pose both challenge and opportunity to teachers. The International Journal of the First Year in Higher Education, 1(1) is the only issue so far in print and includes an article titled “Communicating with first year students; so many channels but is anyone listening?” The abstract includes “A first year group was surveyed about their use and preference for various sources of information. Students were generally positive about the use of social networking and other new online media but strongly preferred more established channels for official academic and administrative information.” Other articles look at teaching practices to better reach first year students. The journal will be published bi-annually. www.biochem.umd.edu/biochem/kahn/teach_res/ Jason Kahn, University of Maryland College Park, has a research group dedicated to the structure, function, and design of protein-DNA complexes. His home page relates this and other interests like the application of phytohormones to improve algal biofuel yield. Kahn's teaching commitments have produced a range of resources that he has been selfless in posting at this site. It is a trove of treasure that needs individual filtering to locate the gems. The menu offers the following choices: 1) Nucleic Acid Sequence, Stability, Structure, and Dynamics, 2) Tools and Tutorials for Molecular Structure, 3) Protein domains and (mis)folding overheads, 4) Student posters, 5) Rasmol/Chime/Jmol installation and use, 6) Materials relating to protein structure and allostery, 7) PDB files of nucleic acids and protein-nucleic acid complexes, 8) Collection of exams, and 9) Literature Searching and EndNote hints. www.endnote.com EndNote from Thomson Reuters is a bibliographic data base utility used by millions to search online bibliographic databases, organize references, images, and PDFs. The data base generated by the user can create bibliographies and figure lists from links inserted into a document. This avoids the chore of typing a reference list after the document is created. EndNote is available for Windows or Macintosh and costs around US$250. I have not used it, but I know from others that it is a great utility and also a great annoyance in seemingly equal measure. Included in Jason Kahn's resources (see above) is the following guide to EndNote. “The program is a combination of database, retrieval engine, and word processor plugin. It can download and organize references and automate the formatting of in-text citations and the creation of bibliographies. It has many other features, like manuscript templates, that I find less useful. Many scientists have a love-hate relationship with EndNote, but writing a scientific document of any length without it or a competing product is foolish. There is a new version every year, but improvements are only incremental. I upgrade only when a must-have OS or Microsoft Office upgrade breaks EndNote, which usually happens. There are four steps to use EndNote. First, you import references into a library. Second, you write a manuscript and insert temporary citations to references in the library. Third, you format the bibliography (this can be done many times, and can even be done as you write, if you like to live dangerously). Fourth, you look at the results carefully and iterate back to steps 1, 2, and 3 as needed”. There is more about Endnote at Jason Kahn's web site complete with screen dumps to help a user. about.com This is a great site for getting lost in serial linking of fascinating facts. The only downside is an annoying intrusion of advertisements, but putting this aside, there is a lot of succinct information easily located here. It is a site to recommend to a student who has done little biochemistry revision and has an examination in 2 days time. About.com was founded in 1996 then acquired by The New York Times Company in 2005. About.com is one of the most visited sites on the internet, with 2.8 million articles on 70,000 topics, written and updated by a network of expert guides. It is not a wiki and the experts seem to be well chosen. You can rapidly get to a menu of choices for Biochemistry and Molecular Biology that leads in many familiar directions. The text of articles is generally well written and backed with enough diagrams to be helpful. The text has hyperlinks to explain most technical terms. One entry that caught both my attention and extended my knowledge was on lycopene. The entry begins: Lycopene (see chemical structure), a carotenoid in the same family as beta-carotene, is what gives tomatoes, pink grapefruit, apricots, red oranges, watermelon, rosehips, and guava their red color. Lycopene is not merely a pigment. It is a powerful antioxidant that has been shown to neutralize free radicals, especially those derived from oxygen, thereby conferring protection against prostate cancer, breast cancer, atherosclerosis, and associated coronary artery disease. It reduces LDL (low-density lipoprotein) oxidation and helps reduce cholesterol levels in the blood. In addition, preliminary research suggests lycopene may reduce the risk of macular degenerative disease, serum lipid oxidation, and cancers of the lung, bladder, cervix, and skin. The chemical properties of lycopene responsible for these protective actions are well-documented. Worth a visit. drnjbmd.wordpress.com/category/biochemistry/ This is a blog site by a medical student offering sound advice to study biochemistry that only a student can offer a fellow traveler. If I offered the same advice as a lecturer, it would be considered unctuous and ignored. I am consistently told that biochemistry is hard to study, so the obvious strategy is to do some hard study. It is all in this blog. esciencenews.com Michael Imbeault obtained his PhD in Quebec Canada by studying retrovirology and bioinformatics. In January 2008, at the end of his study for his PhD, he used his programming skills to create e! Science News. The e! news engine is an automated bot that constantly sifts the web to gather and rank science news from all major science news sources. Imbeault informs us that he used a vector space model and hierarchical clustering to automatically determine which category each news item belongs and the relative importance of each news item. You can target all articles classified as Health Medicine from the top menu. By typing biochemistry into the search engine you will see all of the articles in which an author has declared an affiliation with a Biochemistry Department (a rather crude filter). I was happy enough seeing the totality of the subjects that were shown across many disciplines. A counter at the top keeps updating by informing the visitor how many minutes ago the last article was added. There are also archive options going back over the last year. For an automated system, it works commendably well giving summaries of the items that are linked. For example Core knowledge of tree fruit expands with apple genome sequencing. An international team of scientists from Italy, France, New Zealand, Belgium, and the USA have published a draft sequence of the domestic apple genome in the current issue of Nature. The article leader links to a deeper treatment stored on the eScience site and then there is a link to the source. The site allows for RSS (Really Simple Syndication) feeds into browsers and email systems. Science News is an easy way to keep up to date with science. biochemistryonlinetutor.weebly.com This site is included here as a commentary on the globalization of educational services and not as an endorsement of a private provider. The Weebly host site provides free web sites by offsetting the cost with sponsored pop-ups. If you see a pop-up inviting you to take an interesting series of math puzzles then be warned; it is an advertising ruse. The site is offered by an anonymous Indian provider who you can talk to by telephone in India, or leave your contact details and tutoring requirements. The British Empire spread the English language through many colonies including the US and India. As a citizen of the colony of Australia, I am inclined to believe that I am a privileged speaker and writer of true English. However, there are many legitimate strands of English that cohere in what Robert McCrum has termed Globish [1]. Recently, I needed to remind myself of this diversification in rural Burma when I observed a school teacher giving an English language class on the use of pronouns. What was dubious English language usage by my standards was Burmese-normal, so I did not intervene. One of my mentors told me “we are here to teach biochemistry, not English.” If understanding biochemistry is the reason to take interest in this website then we can make allowances for the Indian variation on Globish. The web page begins: “Welcome to my webpage on Online Tutoring. I do online tutoring on following Subjects for All Levels Biochemistry (list follows). Rates are negotiable, depends on the expertise required and can be decided upon contact.” There are some primary resource materials at the site relating to approaches to study and they are basically sound. This includes the following excerpt. How to Score High in Biochemistry Exams? The best and the essential way to score high in Biochemistry exams are to read more number of biochemistry books and try to know and remember at the least, the key facts of all the topics. Fill-in-the-blank questions are good targets of scoring, especially when the lines may have been reproduced from a good text book. Remembering the mnemonics will be very useful. Important information never changes. A survey of multiple years of exams will show that some things are always important. If a particular topic is asked in more than one exam, then those areas is worth studying. Old exams are to gather intelligence related to what you need to know, how it will be asked, and how much time is needed for studying. When you look at old exams, the question in your mind should be “If the same questions were asked, will I be able to answer it?” Let us look at few strategies to be adopted in the examination hall. If you feel that a very significant point or word should be highlighted, there is no harm in writing it in capital letters or resorting to underlining. For example, when you write a biochemical pathway you can use different colors for enzymes, substrates, cofactors, and final product. Read and understand the question first. Know the scoring pattern of exam questions, and put more energy into questions with more score. If there are pertinent facts or formulas that you are afraid you will forget, then write them down (i.e., do a “brain dump”).

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