Nucleotide sequence and genomic structure analyses of the p70 subunit of the human Ku autoantigen: evidence for a family of genes encoding Ku (p70)-related polypeptides

cDNA encoding the p70 polypeptide subunit of the human Ku autoantigen was isolated. In vitro expression analysis of the cDNA demonstrates that it encodes the entire open reading frame. Nucleotide sequence analysis and comparison to other previously described sequences indicate the existence of several single-nucleotide and amino acid polymorphisms. Southern blot analyses demonstrate the presence of multiple copies of homologous DNA sequences in the human genome. These data support the hypothesis that multiple genes encode a family of Ku(p70)-related polypeptides.     

Determination of isoprostaglandin F2α type III in human urine by gas chromatography–electronic impact mass spectrometry. Comparison with enzyme immunoassay

F₂-Isoprostanes are stable lipid peroxidation products of arachidonic acid, the quantification of which provides an index of oxidative stress in vivo. We describe a method for analysing isoprostaglandin F_2α type III (15-F_2t-IsoP) in biological fluids. The method involves solid-phase extraction on octadecyl endcapped and aminopropyl cartridges. After conversion to trimethylsilyl ester trimethylsilyl ether derivatives, isoprostaglandin F_2α type III is analysed by mass spectrometry, operated in electronic impact selected ion monitoring mode. We have compared enzyme immunoassay (EIA; Cayman, Ann Arbor, MI, USA) to this method with 30 human urine aliquots following the same extraction procedure in order to determine the agreement between both methods. Isoprostaglandin F_2α type III concentrations determined with gas chromatography–mass spectrometry (GC–MS) did not agree with those determined with EIA. Our results suggest that GC–MS and EIA do not measure the same compounds. As a consequence, comparison of clinical results using GC–MS and EIA should be avoided.     

Live imaging of prions reveals nascent PrPSc in cell-surface,raft-associated amyloid strings and webs

Mammalian prions refold host glycosylphosphatidylinositol-anchored PrP^C into β-sheet–rich PrP^Sc. PrP^Sc is rapidly truncated into a C-terminal PrP27-30 core that is stable for days in endolysosomes. The nature of cell-associated prions, their attachment to membranes and rafts, and their subcellular locations are poorly understood; live prion visualization has not previously been achieved. A key obstacle has been the inaccessibility of PrP27-30 epitopes. We overcame this hurdle by focusing on nascent full-length PrP^Sc rather than on its truncated PrP27-30 product. We show that N-terminal PrP^Sc epitopes are exposed in their physiological context and visualize, for the first time, PrP^Sc in living cells. PrP^Sc resides for hours in unexpected cell-surface, slow moving strings and webs, sheltered from endocytosis. Prion strings observed by light and scanning electron microscopy were thin, micrometer-long structures. They were firmly cell associated, resisted phosphatidylinositol-specific phospholipase C, aligned with raft markers, fluoresced with thioflavin, and were rapidly abolished by anti-prion glycans. Prion strings and webs are the first demonstration of membrane-anchored PrP^Sc amyloids.     

The conservation imperative and setting plant taxonomic research priorities in South Africa

For more than a decade it has been internationally recognised that efforts should be made to remedy the concern that taxonomy is an endangered discipline in the grips of rapid decline. In acknowledgement of the perceived continuing marginalisation of taxonomy, the Darwin Declaration recognised the need to enhance the taxonomic capacity of members who are party to the CBD, and beyond. South Africa is one of the most biodiversity rich countries globally, and the unique and rich flora of the country brings with it a significant conservation imperative. Although the country, and southern African subregion for that matter, has a strong history of taxonomic endeavour, stretching back for over a century, it also suffers from a lack of human and other resources to adequately address its taxonomic needs. This inevitably calls for a process of priority-setting to ensure the wise use of available funding. As one example, it is shown that 1,009 indigenous South African plant taxa are regarded as Data Deficient for taxonomic reasons, following the completion of a recent comprehensive Red Listing exercise. Although not the only criterion to be considered when prioritising taxonomic research, efforts focused on these groups represent a significant opportunity for taxonomists to align their work with national priorities.     

Are landscape-based wetland condition indices reflected by invertebrate and diatom communities?

Assessments of wetland condition are generally based on measures of variables related to plants or large animals (birds, fish), and catchment or landscape features. This approach ignores the considerable biodiversity and functional values of small aquatic organisms. The aim of this study was to assess the correspondence between landscape-based indices of wetland condition and the community composition of both aquatic invertebrates and diatoms across a broad range of wetlands in the West Coast region of New Zealand. Aquatic invertebrates and diatoms were sampled from 29 lowland wetlands subject to varying degrees of catchment modification. Wetland condition was assessed independently using two methods: a field-based method to give the Wetland Condition Index, and a GIS-based method that gave an Index of Ecological Integrity. Strong relationships existed between community composition and pH, so we partitioned the community data into groups according to wetland pH. We found only weak relationships between wetland condition scores and invertebrate and diatom communities within each pH group. In most cases, data describing the nutrient status of the water had the strongest influence on invertebrate and diatom communities. Lack of strong associations between measured wetland condition indices and either diatom or invertebrate community composition suggests that neither index was dominated by variables directly influencing the aquatic component of wetland biota. The challenges now are to identify the critical variables, and to develop complementary wetland scoring systems that better reflect the status of small aquatic organisms.     

Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)

Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea.     

Sox11 Reduces Caspase-6 Cleavage and Activity

The apoptotic cascade is an orchestrated event, whose final stages are mediated by effector caspases. Regulatory binding proteins have been identified for caspases such as caspase-3, -7, -8, and -9. Many of these proteins belong to the inhibitor of apoptosis (IAP) family. By contrast, caspase-6 is not believed to be influenced by IAPs, and little is known about its regulation. We therefore performed a yeast-two-hybrid screen using a constitutively inactive form of caspase-6 for bait in order to identify novel regulators of caspase-6 activity. Sox11 was identified as a potential caspase-6 interacting protein. Sox11 was capable of dramatically reducing caspase-6 activity, as well as preventing caspase-6 self- cleavage. Several regions, including amino acids 117–214 and 362–395 within sox11 as well as a nuclear localization signal (NLS) all contributed to the reduction in caspase-6 activity. Furthermore, sox11 was also capable of decreasing other effector caspase activity but not initiator caspases -8 and -9. The ability of sox11 to reduce effector caspase activity was also reflected in its capacity to reduce cell death following toxic insult. Interestingly, other sox proteins also had the ability to reduce caspase-6 activity but to a lesser extent than sox11.