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This Week in PNAS
CHEMISTRY
Tunable graphite layers for hydrogen storage
Serguei Patchkovskii et al. calculate that storing hydrogen gas between layers of graphite may be superior to storage in hydrogen clathrate compounds or between carbon nanotubes. According to the authors, previous calculations have not fully considered the interaction potentials and quantum effects that occur between carbon and hydrogen gas, which has led researchers to overlook graphite's suitability. Patchkovskii et al. modeled interactions between hydrogen and layers of graphite and calculated that hydrogen could be stored at room temperature and at moderate pressures, meeting U.S. Department of Energy goals for storage volume, though not for mass ratio. Most other theoretical and experimental systems have required very cold temperatures or high pressures and meet neither requirement. Spacer molecules interposed between graphite layers could be used to create tunable layers of differing storage properties while keeping out contaminants that could displace the hydrogen. — P.D.
“Graphene nanostructures as tunable storage media for molecular hydrogen” by Serguei Patchkovskii, John S. Tse, Sergei N. Yurchenko, Lyuben Zhechkov, Thomas Heine, and Gotthard Seifert (see pages 10439-10444)
BIOPHYSICS
ALS mutant proteins more stable than thought
Jorge Rodriguez et al. report that mutations associated with amyotrophic lateral sclerosis (ALS) do not affect protein folding as widely as once thought. The findings suggest that the causes of ALS are more complex than simple protein instability, which is proposed as a mechanism for the protein aggregation seen in ALS. Previous research has identified >100 point mutations in the enzyme superoxide dismutase (SOD1) that are thought to underlie ALS. Although previous studies have suggested that instability of SOD1 is a universal characteristic of ALS mutant proteins, this conclusion was based on the study of a small subset of mutations. Rodriguez et al. analyzed the stability and structural characteristics of 20 ALS-associated SOD1 mutations and found that only a small fraction of ALS-mutant apoproteins analyzed were severely destabilized. Some mutants showed normal stability and structure, whereas two of the mutants exhibited greater stability than the wild-type apoprotein. These results suggest that, though apoprotein instability may play a role in ALS etiology, the causes of ALS may involve additional factors related to protein aggregation. — M.M.
“Destabilization of apoprotein is insufficient to explain Cu,Zn-superoxide dismutase-linked ALS pathogenesis” by Jorge A. Rodriguez, Bryan Francis Shaw, Armando Durazo, Se Hui Sohn, Peter A. Doucette, Aram M. Nersissian, Kym F. Faull, Daryl K. Eggers, Ashutosh Tiwari, Lawrence J. Hayward, and Joan Selverstone Valentine (see pages 10516-10521)
ECOLOGY
Hotspots for barnacle reproduction
Heather Leslie et al. identify distinct hotspots of barnacle reproduction along the Oregon coastline and demonstrate that natural variation in “bottom-up” factors, such as phytoplankton availability, contribute to these reproductive hotspots. Although “top-down,” consumer-driven effects on marine communities have been extensively studied by ecologists, relatively little is known about the effect of bottom-up factors. Leslie et al. monitored reproduction in both natural and experimental barnacle populations in two habitats 80 km apart on the Oregon coast, representing areas of high and low primary productivity (as determined by phytoplankton abundance). The researchers found that the sites with high productivity had significantly greater larval production in both natural and experimental populations than did those with lower productivity. Such reproductive hotspots are an important element to consider in designing marine reserves and other marine protected areas, because they could serve as sources of larvae to seed populations in unprotected areas. — M.M.
“Barnacle reproductive hotspots linked to nearshore ocean conditions” by Heather M. Leslie, Erin N. Breck, Francis Chan, Jane Lubchenco, and Bruce A. Menge (see pages 10534-10539)
EVOLUTION
Insertion and deletion events in progressive multiple sequence alignment
Ari Löytynoja and Nick Goldman describe a modification of the traditional DNA sequence alignment algorithm that can distinguish insertion from deletion events. Multiple DNA sequence alignment has been relatively difficult to perform because of the differentiation of insertions and deletions, which can be treated identically in pairwise alignment but are drastically different in progressive multiple alignment. Methods that iterate pairwise alignments can penalize single insertions multiple times, resulting in overmatched sequences or underestimated insertion events. The method developed by Löytynoja and Goldman allows for any substring marked as a gap in previous alignments to be skipped, thus not repeatedly penalizing insertions. The authors illustrate the performance of their algorithm with alignments of real biological sequences, and the results suggest that some previously described insertion-deletion hotspots may actually be artifacts of traditional alignment algorithms. — R.N.
“An algorithm for progressive multiple alignment of sequences with insertions” by Ari Löytynoja and Nick Goldman (see pages 10557-10562)
MEDICAL SCIENCES
Epigenetic differences in identical twins
According to Mario Fraga et al., epigenetic differences between monozygotic (identical) twins may result in phenotypic discordance over time, such as differences in physical appearance or disease susceptibility. Studies of monozygotic twins have helped elucidate the role of environmental factors in disease onset, but the nature of this link is poorly understood. Fraga et al. examined global and gene-specific differences in the epigenetic profiles of 80 sets of identical twins in Spain, ranging from 3 to 74 years in age. The researchers measured genomic DNA methylation (5-methyl-cytosine) content and acetylation levels of histones H3 and H4 in peripheral lymphocytes. In 35% of twin pairs, individual twins had significantly different epigenetic profiles, with differential markers affecting repeat DNA sequences and single-copy genes throughout the genome. Twins with different global epigenetic patterns showed a distinct profile of DNA methylation in their metaphase chromosomes, located in almost all telomeres and select gene-rich regions. Although twins were epigenetically indistinguishable during the early years of life, older twins exhibited marked epigenetic differences resulting in differential gene expression patterns. The greatest epigenetic differences were seen in twin pairs who had spent less of their lifetimes together or had different medical histories. — L.B.
“Epigenetic differences arise during the lifetime of monozygotic twins” by Mario F. Fraga, Esteban Ballestar, Maria F. Paz, Santiago Ropero, Fernando Setien, Maria L. Ballestar, Damia Heine-Suñer, Juan C. Cigudosa, Miguel Urioste, Javier Benitez, Manuel Boix-Chornet, Abel Sanchez-Aguilera, Charlotte Ling, Emma Carlsson, Pernille Poulsen, Allan Vaag, Zarko Stephan, Tim D. Spector, Yue-Zhong Wu, Christoph Plass, and Manel Esteller (see pages 10604-10609)
Figures and Tables
Spatial distribution of hydrogen adsorbed on graphene.
Backbone structure of SOD1 protein.
Oregon coast barnacles.
Analyzing multiple sequence alignments.
DNA methylation patterns of chromosome 1 in 3-year-old (Left) vs. 50-year-old (Right) twins.
