Websites of note

Authors

  • Graham R. Parslow

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, The University of Melbourne, Victoria, Australia Copyright 2013 by The International Union of Biochemistry and Molecular Biology, 42(1):95--98, 2014
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Genetic Alliance

www.geneticalliance.org

Genetic Alliance claims to be the world's leading advocacy organization committed to transforming health through genetics. The extended network includes more than 1,200 disease-specific advocacy organizations, as well as universities, private companies, government agencies, and policy organizations. Founded in 1986, the Alliance has been evolving its advocacy in line with advances in genetics. I arrived at the site while adding to a lecture on Pompe's disease. At that time the US government Discretionary Advisory Committee for Heritable Disorders in Newborns and Children had just recommended the addition of Pompe's Disease to the uniform newborn screening panel (i.e., the Guthrie tests). Recent studies done on samples prepared for Guthrie testing suggests that the prevalence of Pompe's may be as high as 1 in 28,000. The Committee considered both the significant benefit of screening for those with early onset of the condition as well as the need for more studies about the ideal management of those identified as having late onset. The Genetic Alliance took the stance of endorsing the decision to test all neonates. Treatment for Pompe's disease is enzyme replacement therapy by infusion of alpha-1,4-glucosidase every 2 weeks. That treatment currently costs around $100,000 per patient each year. Genetic Alliance had conducted public discussion about the cost and the practicality of countrywide screening for Pompe's and come down in favor. Because all genetic diseases have features in common when it comes to advocacy, the Alliance approaches many genetic diseases in a comparable way. The short video from CEO Sharon Terry at the site presents the case for the mission of Genetic Alliance in a compelling manner. Prominent among the publications listed at the site is the journal Genetic Testing and Molecular Biomarkers. An article that caught my attention in the journal was Do People Want to Know If They Are at Risk for Alzheimer's Disease? Scientific rationalism dictates that people should want to know their genetic predisposition, but the real world is populated with the full range of responses to offers of determining at-risk genotypes.

Baby's First Test

www.babysfirsttest.org

Baby's First Test works with partner organizations to provide educational and training resources for parents and professionals. Genetic Alliance, reviewed above, linked me to this site for an overview of Pompe's disease. All of the genetic diseases commonly tested for in the US are described here. Locating a disease can be either by direct search or by nominating a US state and then linking to the list of diseases tested by that state. Searching for cystic fibrosis (CF) for detail reveals that signs of CF usually start shortly after birth. Early signs of CF include salty sweat; many parents notice a salty taste when kissing their child. This correlates with poor growth and weight gain, constant coughing and wheezing, thick mucus or phlegm and greasy, smelly stools that are bulky and pale colored. The primary information is rather general, but easily read and understood. For professionals more information on CF is provided by a link to the American College of Medical Genetics which in turn produced multiple links to references. Baby's First Test is an easy site to begin an exploration of common medically significant genetic diseases.

Molecular Biology in the US Navy

greenfleet.dodlive.mil/home

The fact sheets at this site reveal that the US possesses 2% of global oil reserves. With only 5% of the world's population, the US consumes about 22% of the world's petroleum supply. To make this work about 60% of the petroleum used in the US comes from overseas and almost half of that comes from OPEC member countries. The Navy uses 75% of its energy afloat and the vast majority of that relies upon liquid petroleum. The US Navy has the goal of cutting its use of fossil fuels in half by 2020 and current alternatives are not practical. Biodiesel can damage equipment and gum up filters and ethanol has low energy density. Stephen Mayfield as director of the UCSD San Diego Center for Algae Biotechnology has been working with the US Navy to develop algae as a viable source for sustainable biofuel (http://biology.ucsd.edu/faculty/mayfield.html). Liquid fossil fuels are plant-derived biomolecules from ancient plants, predominantly algae. Accordingly algae-derived oils have the promise of providing a direct replacement for petroleum fuels. Pilot scale plants are already operational to develop the biotechnology required (http://www.sapphireenergy.com/). If you visit the site for research in the Mayfield lab you will also find a spectrum of projects developing the molecular genetics of green algae. The Mayfield lab has developed expression vectors that allow for robust accumulation of complex mammalian proteins including monoclonal antibodies, mammalian growth factors, and a variety of potential industrial enzymes. Algae are capable of producing these recombinant proteins at very high levels. A promising medical treatment is antibody-toxin fusion proteins from algae that can bind and kill human B-cell lymphomas. Mayfield says in summary “Our continued genetic, biochemical and structural studies should lead to a greater understanding of the mechanism of gene expression in algae, and allow algae to become a viable source for sustainable biofuel and recombinant protein production.”

Fourier Transform Mass Spectrometry

www.bumc.bu.edu/ftms

Advances in scientific understanding require not only asking challenging questions, but also having appropriate instruments to find the answers. The field of proteomics largely exists because of advances in high-performance mass spectrometry instrumentation. This web site is a research lab of the Boston University Medical School and uses Fourier transform mass spectrometry as the highest performance instrumentation available for structural characterization of proteins. The lab is devoted to developing instrumentation and applying the technology. There are a number of simple diagrams of the instrument in addition to explanations of the work and publications from the lab. What brought me to the site was the Isoaspartome page under the research menu, most easily reached directly at http://www.bumc.bu.edu/ftms/research/isoaspartome/. Deamidation of asparagine, and to a lesser extent glutamine, residues is the most common post-translation modification occurring in many proteins as a nonenzymatic spontaneous reaction. Deamidation plays a role in aging, autoimmune disorders (e.g., Celiac disease), neurodegeneration (e.g., Alzheimer's disease), and other diseases. Deamidation can also influence the stability and potency of protein-based drugs. Under physiological conditions, asparagine deamidation proceeds via a succinimide intermediate, which hydrolyzes to form a mixture of aspartate and isoaspartate—Fig. 1. The rate and extent of isoaspartic acid formation can vary widely among proteins, depending on the amino acid sequence and size of the protein. Deamidation of Asn residues has been observed most frequently at Asn-Gly and Asn-Ser sites within proteins. The altered structure of a changed protein may initiate such events as amyloid precipitation and immune recognition.

Figure 1.

The spontaneous generation of isoaspartate. Despite its ubiquity and importance, deamidation is underappreciated and understudied. In part this is due to the difficulty of differentiating the compounds because Asp and isoAsp have the same mass and similar physiochemical properties. Fourier transform mass spectrometry is one technique that can resolve isoaspartate. This figure from http://www.bumc.bu.edu/ftms/research/isoaspartome/. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Scitable

www.nature.com/scitable

Scitable was reviewed for Websites of Note in 2010 when it was a new venture by Nature publications to build an encyclopedic coverage of molecular life science. A web search for information on Langmuir troughs (more later in this review) brought me back to a now mature resource. The home page is superb for presenting interesting science news and offering menus of directions to follow. By way of a site to recommend to life-science students for study and browsing it has few equals. Three major menu choices are People, Groups, and Blogs. Working through these shows that Nature has created its own social media site that allows a student to find a scientist, a friend or simply make comments. There are numerous postings and some of them between students appear more like a dating service, although this may be a bonus to attract students to the site. Under Cell Biology Resources students are invited to explore topic rooms showcasing cell origins and metabolism, proteins and gene expression, subcellular compartments, cell communication, and cell cycle and cell division. An e-textbook is also provided, Essentials of Cell Biology, that develops from an introduction to cell biology for beginning students up to specialized topics for advanced students. Under Create a Classroom a teacher can construct a custom online reading list, threaded discussions, news feeds, and research tools. The online reading list can link to Scitable resources of more than 500 expert-authored, peer-reviewed, explorations of key concepts. The purpose-written reviews aim to provide students with a deep understanding of the scientific method, the experimental tradition, and the nuances of data analysis. Most reviews link to milestone primary literature from Nature, Nature Genetics, and other journals. More than 2,000 teachers worldwide have created Scitable Classrooms for their students using the set-up wizard. Another wizard can create customized eBooks. Returning to the entry point for this website, if you are not sure about the role of Langmuir troughs in revealing the molecular architecture of the cell then you can find a good introduction here. The item Discovering the Lipid Bilayer begins “We are taught that plasma membranes are a typical lipid bilayer, but how do we know this, and who figured it out? Most books mention that membranes have a typical lipid bilayer, but why lipids, why should it be a bilayer, and how was this basic structure determined? Although it is now generally taken for granted that membranes are based on the presence of a lipid bilayer, that was not always the case. Early experiments, often by physicists, led to the understanding that the cell membrane was lipid in nature. A key experiment using the Langmuir trough provided the basis for accepting that the membrane is a bilayer and laid the groundwork for the current model of membrane structure.”

European Food Safety Authority

www.efsa.europa.eu

The European Food Safety Authority was set up in January 2002, following a series of food crises in the late 1990s when contamination and fraudulent packaging eroded confidence in the European food supply. The Authority has a large permanent staff and acts as a risk assessor to formulate policies and legislation common to European Union countries. The Authority assesses the hazards posed by genetically modified crops, pesticides, and feed additives. Due to the diligence of the Authority it is claimed that European consumers are among the best protected and best informed in the world as regards risks in the food chain. In addition to human health, the Authority also considers the possible impact of the food chain on the biodiversity of plant and animal habitats. The enormous literature on food and the safety of food at the site is not readily reached from the home page and a start can be made by entering an item of interest into the search box (e.g. potato scored 709 hits). After entering one search topic you can access searches under the categories Animal health and welfare, Assessment Methodology, Biological hazards, Contaminants, Dietary and chemical monitoring, Emerging Risks, Additives and Products used in Animal Feed, Food Ingredients and Packaging and Genetically Modified Organisms. The home page is excellent for browsing news items and reports and one that caught my attention was on acrylamide. Acrylamide typically forms in starchy food products during high-temperature cooking, including frying, baking, and roasting. It forms from sugars and amino acids in food. Acrylamide has been found in products such as potato crisps, French fries, bread, biscuits, and coffee. It was first detected in foods in April 2002. Occasionally levels exceed current guidelines and determining the level of hazard posed by acrylamide remains a work in progress for the Authority.

Matthew Weintrub's Blog

mattovermatter.com

Matthew Weintrub is taking a major is horticulture and is studying at the Texas A&M Howdy! Farm (studentfarm.tamu.edu) that is an organic, sustainable student run farm affiliated with Texas A&M University. In one news item Weintraub says “I'm a nerd for plant news. Apparently, researchers have announced the debut of a purple super tomato, dubbed Indigo Rose, bred to contain higher than normal levels of antioxidants.” This introduction leads to an edited extract of an article from the NY Daily news, complete with a picture of a deep purple tomato. The purple is due to anthocyanins introduced by classical breeding and possibly conferring better cognitive function and reduced inflammation in consumers. Although plants and nutrition are particular fields of interest, it is clear that Matthew is indulging in his student days to explore the science of just about everything including love and relationships. The site is an enormous blog on topics, mostly summarized under the subject category box that runs alphabetically from acupuncture to yoga with lots of science in-between. Unfortunately, the subject category box is not comprehensive in finding content. Browsing the site will show feature articles of current interest to Matthew and provides a short cut to many of the things that young aspiring scientists should know or contemplate. The categories menu leads to the choices of science, environment, the future, enlightenment, what is happening and wellness. It is almost guaranteed that something in this eclectic compilation will take your interest.

Student Peer Review - PRAZE

peerreview.cis.unimelb.edu.au

The University of Melbourne Australia (the reviewer's host institution), has been a leader in educational innovation for two decades. Consistent institutional support and funding has allowed teams of dedicated educators and support staff to bring projects to productive conclusions. In particular the former Vice Chancellor Alan Gilbert set out in 1996 to build on a strong base of existing projects to “mainstream the digital revolution in education.” The student peer review project headlined here is a computer delivered utility given the acronym PRAZE (Peer Review from A to Z for Education). It was developed to improve the student experience in large classes ranging up to 2,000 students. It was also significant for this project that peer-centered learning could extend the quality of interaction in a cost-effective manner. PRAZE is a web-based peer review system that automates and manages the peer assessment process. After multiple iterations PRAZE has now achieved high usability and functionality. Student comments include “I was surprised by what I got back and how helpful it was.” PRAZE is now ready for adoption by other institutions and is free within Australia.

Edudemic

www.edudemic.com

Started by Jeff Dunn in 2010 to exchange educational resources and philosophies, Edudemic has grown to become one of the leading education technology sites on the web. More than 500,000 visitors per month browse and contribute to the blogs. The visitors are teachers, administrators, and students with an interest in the best use of technology including special interest groups such as iPad users. The site has tools, tips, resources, visuals, and guest posts from dozens of authors around the world. For a relatively young site the intensity of use shows that the format is meeting a need for resource discovery among educators around the world. Jeff Dunn, born Connecticut 1982, has a degree in anthropology and a Harvard Masters in management. He built Edudemic with the assistance of Adobe, Harvard, and MIT. There is no special interest group for biochemistry, but there is a wealth of generic material that supports all teaching. Contributors have posted articles like How To Find The Best Open Course Materials by Katie Lepi. There are teachers guides to technology and learning, Twitter, the flipped classroom and more. This is the world's fastest growing education discussion site, so visit and share the excitement.

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