Myxomycetes in soil

The myxomycetes are a group of protists that form a monophyletic taxon in the phylum Amoebozoa. Evidence of their evolutionary success is the fact that they account for more species (ca. 900 are currently recognized) than the combined total for the rest of the Amoebozoa. Moreover, myxomycetes are present in every terrestrial environment investigated to date and also, as amoebae or flagellated cells, in aquatic environments where they cannot form fruiting bodies. Even if culture-based methods tend to underestimate their occurrence in soil, myxomycetes probably account for ∼50% of soil amoebae. The emergence of molecular-based methods has revolutionized our concepts of biodiversity, but myxomycetes are conspicuously absent from all environmental surveys. Herein we show that this is due to their highly diverging SSU rRNA gene sequences, which contain numerous Group I introns.Further proof comes from a recent study that used a massive sequencing approach without primer bias to amplify RNAs. The results obtained show that the mycetozoans (myxomycetes along with dictyostelids and protostelids) are indeed a dominant group of soil protozoans.     

Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis

The protein modifier ubiquitin is a signal for proteasome-mediated degradation in eukaryotes. Proteasome-bearing prokaryotes have been thought to degrade proteins via a ubiquitin-independent pathway. We have identified a prokaryotic ubiquitin-like protein, Pup (Rv2111c), which was specifically conjugated to proteasome substrates in the pathogen Mycobacterium tuberculosis. Pupylation occurred on lysines and required proteasome accessory factor A (PafA). In a pafA mutant, pupylated proteins were absent and substrates accumulated, thereby connecting pupylation with degradation. Although analogous to ubiquitylation, pupylation appears to proceed by a different chemistry. Thus, like eukaryotes, bacteria may use a small-protein modifier to control protein stability.     

Three-dimensional structure of herpes simplex virus from cryo-electron tomography

Herpes simplex virus, a DNA virus of high complexity, consists of a nucleocapsid surrounded by the tegument-a protein compartment-and the envelope. The latter components, essential for infectivity, are pleiomorphic. Visualized in cryo-electron tomograms of isolated virions, the tegument was seen to form an asymmetric cap: On one side, the capsid closely approached the envelope; on the other side, they were separated by approximately 35 nanometers of tegument. The tegument substructure was particulate, with some short actin-like filaments. The envelope contained 600 to 750 glycoprotein spikes that varied in length, spacing, and in the angles at which they emerge from the membrane. Their distribution was nonrandom, suggesting functional clustering.     

Reactions at interfaces as a source of sulfate formation in sea-salt particles

Understanding the formation of sulfate particles in the troposphere is critical because of their health effects and their direct and indirect effects on radiative forcing, and hence on climate. Laboratory studies of the chemical and physical changes in sodium chloride, the major component of sea-salt particles, show that sodium hydroxide is generated upon reaction of deliquesced sodium chloride particles with gas-phase hydroxide. The increase in alkalinity will lead to an increase in the uptake and oxidation of sulfur dioxide to sulfate in sea-salt particles. This chemistry is missing from current models but is consistent with a number of previously unexplained field study observations.     

Formation of hollow nanocrystals through the nanoscale Kirkendall effect

Hollow nanocrystals can be synthesized through a mechanism analogous to the Kirkendall Effect, in which pores form because of the difference in diffusion rates between two components in a diffusion couple. Starting with cobalt nanocrystals, we show that their reaction in solution with oxygen and either sulfur or selenium leads to the formation of hollow nanocrystals of the resulting oxide and chalcogenides. This process provides a general route to the synthesis of hollow nanostructures of a large number of compounds. A simple extension of the process yielded platinum-cobalt oxide yolk-shell nanostructures, which may serve as nanoscale reactors in catalytic applications.     

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.