The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.

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Mfold web server for nucleic acid folding and hybridization prediction

A procedure for the isolation of deoxyribonucleic acid from micro-organisms

http://www.protocol-online.org/forums/index.php?app=core&module=attach&section=attach&attach_id=2894

Studies on transformation of Escherichia coli with plasmids

3.2.3. Hydroformylation 2467 3.2.4. Dimerization 2468 3.2.5. Oxidative Cleavage and Ozonolysis 2469 3.2.6. Metathesis 2470 4. Terpenes 2472 4.1. Pinene 2472 4.1.1. Isomerization: R-Pinene 2472 4.1.2. Epoxidation of R-Pinene 2475 4.1.3. Isomerization of R-Pinene Oxide 2477 4.1.4. Hydration of R-Pinene: R-Terpineol 2478 4.1.5. Dehydroisomerization 2479 4.2. Limonene 2480 4.2.1. Isomerization 2480 4.2.2. Epoxidation: Limonene Oxide 2480 4.2.3. Isomerization of Limonene Oxide 2481 4.2.4. Dehydroisomerization of Limonene and Terpenes To Produce Cymene 2481

Chemical Routes for the Transformation of Biomass into Chemicals

High-performance liquid chromatography is a promising alternative for determining the G+C content of bacterial deoxyribonucleic acid (DNA). The method which we evaluated involves enzymatic degradation of the DNA to nucleosides by P1 nuclease and bovine intestinal mucosa alkaline phosphatase, separation of the nucleosides by high-performance liquid chromatography, and calculation of the G+C content from the apparent ratios of deoxyguanosine and thymidine. Because the nucleosides are released from the DNA at different rates, incomplete degradation produces large errors in the apparent G+C content. For partially purified DNA, salts are a major source of interference in degradation. However, when the salts are carefully removed, the preparation and degradation of DNA contribute little error to the determination of G+C content. This method also requires careful selection of the chromatographic conditions to ensure separation of the major nucleosides from the nucleosides of modified bases and precise control of the flow rates. Both of these conditions are achievable with standard equipment and C18 reversed-phase columns. Then the method is precise, and the relative standard deviations of replicate measurements are close to 0.1%. It is also rapid, and a single measurement requires about 15 min. It requires small amounts of sample, and the G+C content can be determined from DNA isolated from a single bacterial colony. It is not affected by contamination with ribonucleic acid. Because this method yields a direct measurement, it may also be more accurate than indirect methods, such as the buoyant density and thermal denaturation methods. In addition, for highly purified DNA, the extent of modification can be determined.

Precise Measurement of the G+C Content of Deoxyribonucleic Acid by High-Performance Liquid Chromatography

Heavy-isotope-labeled DNA has been used to study strand separation and recombination. The rate at which 14 N− 15 N biologically half-labeled DNA can be made to separate into subunits corresponds very closely to what has been predicted for the rate of unwinding of the strands of a double helix. The use of a phosphodiesterase from E. coli ( Lehman, 1960 ) which selectively attacks single-stranded DNA has made it possible to remove unmatched single chain ends from renatured DNA and reduce the remaining differences between renatured and native DNA. A mixture of heavy-isotope-labeled and normal bacterial DNA was taken through a heating and annealing cycle, treated with the phosphodiesterase and examined by cesium chloride density-gradient centrifugation. Three bands were observed, corresponding to heavy renatured, hybrid, and light renatured DNA. As would be expected for random pairing of complementary strands, the amount of the hybrid was double that of either the heavy or the light component. It has thus been demonstrated that the strands which unite in renaturation are not the same strands that were united in the native DNA but instead are complementary strands originating in different bacterial cells. The formation of hybrids has been possible only where the heavy and normal DNA samples have a similar overall base composition. It has also been shown for DNA samples isolated from bacteria of different genera in a case where genetic exchange by conjugation has been demonstrated. The evidence for the parallelism between genetic compatibility and the formation of DNA hybrids in vitro has led to the proposal that organisms yielding DNA which forms hybrid molecules are genetically and taxonomically related.

The Formation of Hybrid DNA Molecules and their use in Studies of DNA Homologies

Nuclear weapons stockpiles still represent the biggest threat to civilization.

The forgotten menace

Dædalus Fall 2009 The 1⁄2rst 40 years of the nuclear age, dominated by the Cold War, witnessed the staggering buildup of nuclear weapons in U.S. and Russian arsenals. In 1987 the arsenals reached a combined total of about 70,000. U.S. weapons peaked at 32,000 in 1966; Soviet weapons peaked somewhere between 40,000 and 50,000 in 1986. Equally remarkable has been the decline from those heights: both countries, having reduced their stockpiles to 10,000 by 2002, agreed to cut the number of “operationally deployed strategic warheads” to 2,200 by 2012. The United States has already reached this limit, but retains 700 tactical weapons and a reserve of 2,500 active and inactive weapons, not treaty-limited, making for a grand total of 5,200. While comparable data are not available from Russia, it is likely that their stockpile will soon approach a similar level, representing the lowest number of weapons between the United States and Russia since the early days of the buildup, around 1959. A massive exchange between U.S. and Soviet nuclear arsenals during any part of the past half-century would have risked near or total destruction of the world’s civilization. That this did not happen was mainly due to the fear that resorting to use of such weapons by one side would quickly lead to an escalation, since each side would seek to destroy the other’s not-yet-used forces, as well as to retaliate in response to destruction already under way. The level of devastation that would have occurred is unimaginable, but several models have attempted to describe some of the consequences. One model, for example, concluded that to destroy 25 percent of the population of Russia, the United States, Britain, France, and Germany would need fewer than 250 large weapons. Millions more fatalities and further disruption of transportation, energy supply, communications, food supplies, and medical aid, as well as the breakdown of government, commerce, trade, social order, and civil life, would follow, while delayed fatalities and illnesses from radioactive fallout would peak and then subside only slowly over centuries.1 Alas, the potential for this level of destruction still remains, despite the seven-fold reduction in U.S. and Russian weapons that has occurred. Therefore a primary goal in the next decades must be to remove this risk of near global self-destruction by drastically reducing nuclear forces to a level where this outcome is not possible, but where a Paul Doty

The minimum deterrent & beyond

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Paul Doty

Papers

The Formation of Hybrid DNA Molecules and their use in Studies of DNA Homologies

The forgotten menace

The minimum deterrent & beyond

Baltimore's unanswered questions

A Freeze on Strategic Delivery Systems