July 2004

Have you ever risked disapproval? Have you ever risked a belief? ... real courage is risking something that might force you to rethink your thoughts and suffer change and stretch consciousness. Real courage is risking one's clichés.- From Another Roadside Attraction by Tom RobbinsI recently attended BIO 2004, the annual jamboree of the biotech indus try. The optimism and energy of the place invigorated me as industry pioneers shared their visions of the future and I learned about new techno

Brad FitzpatrickAlively and sometimes acrimonious discussion is raging in scientific and publishing circles over the issue of "open access" to the content of scientific journals, where all papers published in a journal are available, at no charge, to everyone from the day they appear in print. Under this model, the costs associated with publishing are borne solely by the authors, or more likely by their funding sources; readers do not pay for access.The American Society for Biochemistry and Mole

I read the Closing Bell "A Way of Life (Almost) Going up in Smoke"1 with great interest. But may I please draw your attention towards something that has hurt my feelings and, possibly, the feelings of many Muslims around the world.The article stated with regard to smoking that "for Muslims, confusion reigns because the Prophet Muhammad ... said nothing about tobacco ... because he probably did not know it existed." This reflects a lack of knowledge of the Islamic Jurisprudence and the true natur

Although numerous scientists and stakeholders recognize a need for increased security measures at microbiological laboratories, Richard Gallagher speaks for many by asking, "Is it possible that we could have a more measured public debate? A more objective assessment of the threat?"1We contend that biosecurity measures at bioscience institutions should be based on an intellectually defensible risk-assessment approach, which evaluates the probability and consequences that biological material would

"Toothsome Directions in Research"1 focuses on the idea that "the mouth harbors oral infections that may negatively affect one's overall health," ignoring that this belief resulted in unfounded tooth extractions in the past.2 Although many studies exist on the trendy systemic-oral disease connection, little evidence supports a causal link between oral infections and poor pregnancy outcomes or cardiovascular disease, and fairly good epidemiologic arguments challenge it.34The main reason for the c

Some European imports have never been welcomed with open arms in the United States, particularly in these days of EU trade wars and Freedom Fries. The rabid tactics increasingly used by a hard core of animal-rights extremists must rank among the least welcome trends to cross the Atlantic in recent times.A clear sign that something new was afoot came in early June during the Biotechnology Industry Organization meeting in San Francisco. Animal and ecological rights groups, said FBI special agent P

Andrzej KrauzeIf you're one of the hundreds of thousands of regular BioMedNet users, you'll know that the Web site went dark on June 30, after nine years of creating a large and vibrant community of life scientists, based on content such as a bookstore, mouse knockout database, PubMed, and a biomedical database. (If you're a regular reader of The Scientist Daily News online, you'll know that we reported the coming demise in December.) The abridged story of the once wildly successful site is wort

Climate-change predictions are fraught with uncertainty. To build meaningful models of temperature and sea-level changes throughout the 21st century, researchers contributing to the Intergovernmental Panel on Climate Change's (IPCC) Third Assessment Report produced a set of four storylines that qualitatively assess social, economic, cultural, and political climes throughout the 21st century. These are developed into quantitative greenhouse-gas emission models called the Special Report on Emissio

BRINGING ON THE NEXT ICE AGE?Dee Breger, Drexel UniversityAssumptions that tiny diatoms such as the ones shown above could fix carbon from the air and sink it to the bottom of the ocean have been hard to prove.The US Department of Energy has taken an interest in carbon sequestration, but a grand scheme to induce thick blooms of carbon-fixing algae has yet to bear fruit in early studies. The DOE directs a large share of its global warming budget to carbon-sequestration research, drawing on biolog

A BUSY HORMONE:© 2001 Annual ReviewsEstrogen's direct genomic effects are mediated by the nuclear form of the estrogen receptors ERα or ERβ which associate with the Estrogen Response Element (ERE) or the fos/jun heterodimers that bind AP1 sites. Indirect genomic mechanisms include activation of ER-linked second messenger systems such as AC/PKC, cAMP/PKA and MAPK/ERK. Ras activates Raf, leading to sequential phosphorylation and activation of MAPK/ERK which interacts directly with n

DELETION BY DESIGN:Courtesy of Guci GiaeverThe deletion cassette module used to delete each yeast gene contains two 74-basepair tags upstream and downstream (UPTAG and DNTAG) of the KanMX gene, which confers resistance to the drug geneticin. UPTAG and DNTAG contain 18 basepairs of genomic sequence to flank the yeast's open reading frame, and U1 and U2, or D1 and D2 PCR primers for amplifying a unique 20-basepair TAG region-the so-called molecular barcode. A second round of PCR adds 45 base-pairs

Courtesy of Pau Atela, Smith CollegeMost flowering plants arrange their leaves and petals in spirals around their stems. And in most species, the angle between successive elements is close to the so-called golden angle, 137.5 degrees, a number derived from mathematic theory that correlates to artistic aesthetics and biological patterning. This convergence has puzzled researchers for 250 years.A German team now suggests that the arrangement minimizes the shadow each leaf casts on those below it,

Cindy MageeTrying to segregate disorganized chromosomes is a feat akin to unpacking tangled Christmas lights. But through largely unknown processes, proteins called condensins help organize DNA during cell division. Using optical-trap microscopy, researchers recently analyzed an Escherichia coli condensin, MukBEF, which works like a "molecular Velcro," says Carlos Bustamante, a professor at the University of California, Berkeley.Bustamante and colleagues mechanically manipulated a single molecul

These papers were selected from multiple disciplines from the Faculty of 1000, a Web-based literature awareness tool http://www.facultyof1000.com.M. Matsuzaki et al., "Genome sequence of the ultrasmall unicellular red alga Cyandidioschyzon merolae 10D," Nature, 428:653–7, April 8, 2004.Cyanidioschyzon is an extremophilic alga that lives in conditions of high temperature and low pH. It has either maintained ancestral eukaryotic features or, more likely, has become simplified due to its spec

Courtesy of VistaLab TechnologiesMt. Kisco, NY-based VistaLab http://www.vistalab.com is bringing ergonomics to the high-throughput laboratory. Like its single-channel predecessor, the new, fully motorized Ovation BioNatural 12-channel pipettes are designed to place the user's hand, arm, and elbow in the proper ergonomic position.Company president Richard Scordato points out that standard multichannel pipettes, both manual and electronic, require a great deal of force for tip acquisition and eje

Whether aggregation of normal protein into tangles is the cause or effect of neurodegenerative diseases such as Alzheimer and Creutzfeldt-Jakob remains unclear. Nevertheless, a number of biotechnology companies are looking at ways to prevent seeding of these proteins. St. Louis-based Novactyl recently was awarded US patent 6,743,771 for a method of blocking protein aggregation using picolinic acid.The compound exhibits transition metal chelating activity, and according to the patent, "It is beli

Courtesy of CellwareThere are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms

Courtesy of AgilentPerhaps no technology better embodies the spirit of the post-genomics age than the microarray. If genome sequencing projects listed the parts that make up an organism – be it a mouse, a fly, or a human – DNA microarrays, or "biochips," provide the first real application for that information.Microarrays are addressable assemblies of nucleotide sequences tethered to a solid surface, each of which represents a single gene, splice variant, or other DNA element. Armed w

Microarray density continues to climb. In the past year, several companies have compressed the entire protein-coding portion of the human genome onto a single chip – that's some 30,000 to 40,000 unique gene sequences per slide. One company has reduced its arrays to the size of microtiter-plate wells, for use in high-throughput biochip analysis. And arrays to genotype 100,000 single nucleotide polymorphisms (SNPs) at once have also come to market."In the next few months, you're going to see

With the ever-increasing density of microarrays comes a need for moresensitive and high-throughput ways to read the resulting data. Arrays contain tens of thousands of 50- to 150-μm-diameter spots per square centimeter, and the vast amount of information they produce has pushed imaging and scanning equipment to its limits.Several recent advances promise to improve the sensitivity, speed, and accuracy of microarray readers. Scanners are becoming more versatile, able to read a broader range o

Microarray technology allows the simultaneous monitoring of expression levels of thousands of genes and even whole genomes. But the experiments themselves represent only the opening act. The grand finale, so to speak, is the data analysis. Sophisticated statistical software and tools exist, but the sheer volume of data, the likes of which are unfamiliar to most biologists (and most statisticians), still represents the primary hurdle in DNA microarray research."Five years ago, there were no stati

Fifteen years into the microarray revolution, biochip images – row upon row of red and green spots on a field of black – have become as ubiquitous as DNA gels once were.But how are those pictures generated? Arrays are imaged using one of two classes of equipment: array imagers and array scanners. Both use lasers to excite the fluorphors on the chip, but where imagers capture a snapshot of the glowing array using a charge-coupled device (CCD camera), scanners read the chip point-by-po

The National Institutes of Health spent more than 90% of its $27.17 billion FY 2003 budget on grants to support R&D activities in the United States. This was spread among nearly 2,900 institutions and morethan 52,000 awards.- Ken KostelSources: National Institutes of Health, American Association for the Advancement of Science

Courtesy of Malta Tourism AuthorityRichard Muscat rarely tunes in to the daily news, but while tending to his children last November, he overheard a TV newscast that stopped him. The prime minister had set aside €800,000 to launch a national research program. For the first time ever, the government allocated money to research. "Thank heavens," Muscat recalls thinking. "They have finally done it."Muscat, a neuroscientist at the University of Malta, and his colleagues had lobbied the Maltese

Arti RaiCourtesy of Duke Law SchoolThe decades of freedom from liability for patent infringement may be over for US universities and research institutes, unless the National Research Council (NRC) gets its way. In the past, universities could use patented techniques and devices without a license, because of the so-called experimental use exemption. In other words, patents could be infringed in academic pursuits.Action in the federal courts has closed that loophole. Instead of letting universitie

Many sources such as books, Web sites, and workshops provide advice on writing grants. When you sit down to work on your grant, though, the advice may not propel you from theory to application. The trouble is, most sources supply generic help, written for anonymous grant writers. Here, you'll learn how to find personalized help that is often nearby.Before getting specific, let's consider four general suggestions. First, look to your institution's grants office. Grants specialists can help you fi

File PhotoThe European Commission (EC) is putting an ever increasing emphasis on excellence and mobility of researchers. Yet, according to Euroscience board member Christine Heller del Riego, the proportion of mobile scientists in Europe is low. What is holding scientists back?A long list of obstacles faces the migrant scientist, especially if children are involved. Moving from one country to another means not only finding a new place to live, but also coming to grips with different tax and heal

When I was learning biology many years ago, structures and disorders named for their discoverers not only eased memorization, but added an historical dimension that I sorely miss. Turner's syndrome, for example, conjured up an immediate image of the good Dr. Henry Turner. At a medical conference in 1938, he described seven young women in his endocrinology practice with the same strange set of symptoms: folds of skin on the back of the neck, malformed elbows, and lack of secondary sexual characte