In This Issue
CHEMISTRY, APPLIED BIOLOGICAL SCIENCES
Four-color DNA sequencing
Accurate high-throughput DNA sequencing techniques are required for genomic research. Jingyue Ju et al. have developed a technique for DNA sequencing by synthesis, which uses cleavable fluorescent nucleotide reversible terminators. Instead of attaching fluorophores to the 3′-OH end of nucleotides, as others have attempted previously, Ju et al. attached cleavable fluorophores to the base of the nucleotide with a small allyl linker. The same allyl moiety was also used to cap the 3′-OH of the nucleotide. Each of the four DNA nucleotides was labeled with a different fluorophore. The modified nucleotides were added to the chip-immobilized DNA to be sequenced and were incorporated by DNA polymerase into the growing DNA strand. Cleaving both of the allyl moieties to remove the fluorophore and free the 3′-OH group facilitated further nucleotide addition to the growing DNA strand. Using a four-color fluorescent scanner, template sequences could be read by the unique color of the fluorophores released from the incorporated nucleotides. Up to 20 continuous DNA bases, including repeated nucleotides, could be read on a chip. This sequencing technique could be extended to read more complicated and longer DNA sequences, the authors say. — P.D.
Four-color fluorescence images for each sequencing step on a chip.
“Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators” by Jingyue Ju, Dae Hyun Kim, Lanrong Bi, Qinglin Meng, Xiaopeng Bai, Zengmin Li, Xiaoxu Li, Mong Sano Marma, Shundi Shi, Jian Wu, John R. Edwards, Aireen Romu, and Nicholas J. Turro (see pages 19635–19640)
ENVIRONMENTAL SCIENCES, SUSTAINABILITY SCIENCES
Atmospheric brown clouds and rice harvests
Widespread atmospheric brown clouds caused by air pollution reduce the amount of solar radiation reaching the earth's surface while increasing atmospheric solar heating. The dryer and dimmer surface conditions that result could adversely affect important food crops. One of the largest of these clouds hovers over the North Indian Ocean and the Indian subcontinent, one of the world's major rice-producing regions. To examine the effects of these clouds on rice harvests, Maximilian Auffhammer et al. constructed a model that combines historical Indian rice-harvest data with an ocean–atmosphere-coupled climate model. Brown cloud data were obtained from the Indian Ocean Experiment conducted by V. Ramanathan with >200 international colleagues during the late 1990s. The authors found that historical rice harvests would have been larger in the absence of the clouds, and larger still if reductions in the clouds were accompanied by reductions in greenhouse gases. Contrary to previous concerns that reducing the brown clouds could diminish harvests by unveiling the warming effects of greenhouse gases, these results suggest that reductions in these clouds, alone or in combination with reductions in greenhouse gases, would benefit rice harvests in India. — M.M.
Satellite image of atmospheric brown cloud.
“Integrated model shows that atmospheric brown clouds and greenhouse gases have reduced rice harvests in India” by Maximilian Auffhammer, V. Ramanathan, and Jeffrey R. Vincent (see pages 19668–19672)
BIOCHEMISTRY, PHYSICS
Molecular movement in thermodiffusion
In an aqueous solution, molecules such as DNA typically drift toward the colder region of a temperature gradient, an effect called thermodiffusion. Stefan Duhr and Dieter Braun developed a general, microscopic theory for thermodiffusion that depends on the effects of solvation entropy. Using an all-optical microfluidic fluorescence method that allows the measurement of thermodiffusion without artifacts induced by thermal convection, the authors determined the effects of salt concentration and temperature on DNA and polystyrene beads over a large size range. The technique could also be used to calculate the charge of the molecules. For both the DNA and the beads, the negative entropy of ionic shielding explained thermophobicity, whereas at lower temperatures, the increasing positive entropy of hydration caused them to become thermophilic. Because thermodiffusion allows the microscale manipulation of miniscule particles, the authors' findings may lead to powerful all-optical screening methods for biomolecules and colloids over a size range smaller than current electrophoresis methods. — F.A.
“Why molecules move along a temperature gradient” by Stefan Duhr and Dieter Braun (see pages 19678–19682)
BIOPHYSICS
Visualizing membrane fusion by real-time fluorescence
A highly conserved family of proteins called SNAREs mediates membrane fusion in eukaryotic cells, which is integral to biological processes such as exocytosis and vesicular trafficking. Tae-Young Yoon et al. developed a real-time fluorescence technique to observe SNARE-driven fusion at the level of single liposomes. By incorporating fluorescent donor/acceptor pairs into liposomes containing yeast SNAREs, the authors tracked proteoliposome fusion by FRET microscopy. Yoon et al. identified kinetic transitions between intermediate states including hemifusion, a metastable membrane structure in which the outer membrane leaflets are merged while the inner leaflets remain intact, followed by a flickering of fusion pores. This research may aid in the understanding of SNARE-mediated membrane fusion events such as the Ca2+-triggering mechanism in neuronal synapses. — F.A.
SNARE-induced liposomal membrane fusion.
“Multiple intermediates in SNARE-induced membrane fusion” by Tae-Young Yoon, Burak Okumus, Fan Zhang, Yeon-Kyun Shin, and Taekjip Ha (see pages 19731–19736)
IMMUNOLOGY
Lupus autoantibodies may promote cognitive defects
Although treatment regimens have prolonged the life of patients with systemic lupus, such therapy has also increased secondary complications such as neuropsychiatric lupus, a cognitive defect that frequently manifests as memory loss. Studies in mice indicate that autoantibodies that cross-react with DNA and the NMDA receptor can cause neuronal damage. Czeslawa Kowal et al. examined whether lupus autoantibodies contribute to neuropsychiatric lupus. The authors injected human serum with reactivity to DNA and the NMDA receptor from lupus patients into mice. The serum induced brain damage and cognitive deficiencies in the mice when the blood–brain barrier was breached using lipopolysaccharide. Impairment was principally centered in the hippocampus. IgG antibodies from a human patient's brain tissue were also able to bind the NMDA receptor and induce neuron death when injected into mice. These findings show that lupus patients can potentially have circulating levels of autoantibodies capable of causing neuronal damage if they breach the blood–brain barrier. — N.Z.
Reactivity of IgG from brain of lupus patient.
“Human lupus autoantibodies against NMDA receptors mediate cognitive impairment” by Czeslawa Kowal, Lorraine A. DeGiorgio, Ji Y. Lee, Mark A. Edgar, Patricio T. Huerta, Bruce T. Volpe, and Betty Diamond (see pages 19854–19859)
