An autoinhibitory mechanism for nonsyntaxin SNARE proteins revealed by the structure of Ykt6p

Ykt6p is a nonsyntaxin SNARE implicated in multiple intracellular membrane trafficking steps. Here we present the structure of the NH2-terminal domain of Ykt6p (Ykt6pN, residues 1 to 140). The structure of Ykt6pN differed entirely from that of syntaxin and resembled the overall fold of the actin regulatory protein, profilin. Like some syntaxins, Ykt6p adopted a folded back conformation in which Ykt6pN bound to its COOH-terminal core domain. The NH2-terminal domain plays an important biological role in the function of Ykt6p, which in vitro studies revealed to include influencing the kinetics and proper assembly of SNARE complexes.     

Community proteomics of a natural microbial biofilm

Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.     

Extracellular proteins limit the dispersal of biogenic nanoparticles

High-spatial-resolution secondary ion microprobe spectrometry, synchrotron radiation-based Fourier-transform infrared spectroscopy, and polyacrylamide gel analysis demonstrated the intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an example of extracellular biomineralization. Experiments involving synthetic zinc sulfide nanoparticles and representative amino acids indicated a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially derived extracellular proteins can limit the dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow.     

Lineages of acidophilic archaea revealed by community genomic analysis

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.     

MAGNETIC RESONANCE ARTHROGRAPHY OF THE CANINE STIFLE JOINT TECHNIQUE AND APPLICATIONS IN ELEVEN MILITARY DOGS

The stifle joints of eleven military working dogs were evaluated using conventional magnetic resonance (MR) imaging and MR arthrography. A protocol optimizing MR imaging of the canine stifle joint is discussed, as well as potential uses for administration of intra-articular gadolinium. The technique for performing MR arthrography is described, and post-contrast image findings are reviewed. MR arthrography was performed by using an intra-articular injection of diluted gadolinium. Consistently good quality images were obtained, and no complications were clinically detected following MR arthrography. Cranial cruciate ligament abnormalities were seen in six dogs, meniscal abnormalities were visualized in nine menisci, and synovitis and medial ligament strain were seen in eight dogs. Surgical and post-mortem confirmation of these findings is discussed in seven dogs. Although MR arthrography adds an invasive procedure to conventional MR imaging, it can provide useful information on pathologic changes in the canine stifle joint.     

Characterisation of peaty materials from organic soils (histosols) in England and Wales

Eighty-eight samples of peaty materials from a wide range of organic soil profiles (Histosols) were classified as fibric, mesic or humic using classes defined by field observations of unrubbed and rubbed fibre contents. A second method of classification based on a diagram using laboratory measured rubbed fibre content (RFp) and absorbance (550 nm) of pyrophosphate extract (Abs) was used and the two classifications compared. Pyrophosphate index and 11 other properties of the samples were measured in the laboratory and their class values were studied for the two classifications. Overlap of class values for non-definitive properties was common. Two laboratory techniques for measuring rubbed fibre content were compared with a field assessment. A method for measuring water content and extrudability was found to be a promising method for characterising peat samples.     

Monoclonal antibodies raised to human cells--specificity for pig leukocytes.

A total of 27 monoclonal antibodies raised to human targets were included in the present Pig CD workshop. 14 of these had been tested in previous workshops and had been reported as cross-reactive, a further 13 had been reported as cross-reactive during the Human Leukocyte Differentiation Antigens Workshop VI (HLDA VI) and/or by the donor (a commercial company submitting these mAb for validation by the workshop community). Of the 27 antibodies, three antibodies with previously reported reactivity for pig cells were eliminated from the workshop following preliminary tests due to lack of reactivity. Nine antibodies, although initially positive, gave inconsistent results during the course of the workshop. We found consistent reactivity for 15 antibodies. However, the cellular distribution of the target molecules on pig and human cells was shown to be different for three of these antibodies. These findings have important implications for the usefulness of these antibodies as research tools in the pig.     

Aggregation-based crystal growth and microstructure development in natural iron oxyhydroxide biomineralization products

Crystals are generally considered to grow by attachment of ions to inorganic surfaces or organic templates. High-resolution transmission electron microscopy of biomineralization products of iron-oxidizing bacteria revealed an alternative coarsening mechanism in which adjacent 2- to 3-nanometer particles aggregate and rotate so their structures adopt parallel orientations in three dimensions. Crystal growth is accomplished by eliminating water molecules at interfaces and forming iron-oxygen bonds. Self-assembly occurs at multiple sites, leading to a coarser, polycrystalline material. Point defects (from surface-adsorbed impurities), dislocations, and slabs of structurally distinct material are created as a consequence of this growth mechanism and can dramatically impact subsequent reactivity.