The cellular prion protein and its role in Alzheimer disease

The cellular prion protein (PrP^C) is a membrane-bound glycoprotein especially abundant in the central nervous system (CNS). The scrapie prion protein (PrP^Sc, also termed prions) is responsible of transmissible spongiform encephalopathies (TSE), a group of neurodegenerative diseases which affect humans and other mammal species, although the presence of PrP^C is needed for the establishment and further evolution of prions.The present work compares the expression and localization of PrP^C between healthy human brains and those suffering from Alzheimer disease (AD).In both situations we have observed a rostrocaudal decrease in the amount of PrP^C within the CNS, both by immunoblotting and immunohistochemistry techniques. PrP^C is higher expressed in our control brains than in AD cases. There was a neuronal loss and astogliosis in our AD cases. There was a tendency of a lesser expression of PrP^C in AD cases than in healthy ones. And in AD cases, the intensity of the expression of the unglycosylated band is higher than the di- and monoglycosylated bands.With regards to amyloid plaques, those present in AD cases were positively labeled for PrP^C, a result which is further supported by the presence of PrP^C in the amyloid plaques of a transgenic line of mice mimicking AD.The work was done according to Helsinki Declaration of 1975, and approved by the Ethics Committee of the Faculty of Medicine of the University of Navarre.Key words: cellular prion protein, Alzheimer disease, transgenic mice     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Identification of DNA sequence variation in Campylobacter jejuni strains associated with the Guillain-Barré syndrome by high-throughput AFLP analysis

Background  

Campylobacter jejuni is the predominant cause of antecedent infection in post-infectious neuropathies such as the Guillain-Barré (GBS) and Miller Fisher syndromes (MFS). GBS and MFS are probably induced by molecular mimicry between human gangliosides and bacterial lipo-oligosaccharides (LOS). This study describes a new C. jejuni-specific high-throughput AFLP (htAFLP) approach for detection and identification of DNA polymorphism, in general, and of putative GBS/MFS-markers, in particular.     

A Novel Mechanism for SUMO System Control: Regulated Ulp1 Nucleolar Sequestration

The small ubiquitin-related modifiers (SUMOs) are evolutionarily conserved polypeptides that are covalently conjugated to protein targets to modulate their subcellular localization, half-life, or activity. Steady-state SUMO conjugation levels increase in response to many different types of environmental stresses, but how the SUMO system is regulated in response to these insults is not well understood. Here, we characterize a novel mode of SUMO system control: in response to elevated alcohol levels, the Saccharomyces cerevisiae SUMO protease Ulp1 is disengaged from its usual location at the nuclear pore complex (NPC) and sequestered in the nucleolus. We further show that the Ulp1 region previously demonstrated to interact with the karyopherins Kap95 and Kap60 (amino acids 150 to 340) is necessary and sufficient for nucleolar targeting and that enforced sequestration of Ulp1 in the nucleolus significantly increases steady-state SUMO conjugate levels, even in the absence of alcohol. We have thus characterized a novel mechanism of SUMO system control in which the balance between SUMO-conjugating and -deconjugating activities at the NPC is altered in response to stress via relocalization of a SUMO-deconjugating enzyme.The small ubiquitin-related modifiers (SUMOs) are a family of evolutionarily conserved polypeptides that are conjugated to protein targets via the concerted action of SUMO-specific E1 (activation), E2 (conjugation), and E3 (ligase) enzymes to effect changes in subcellular localization, half-life, or target activity. A family of SUMO-specific proteases act to remove the modifier from conjugates (8, 20). The SUMO system has been implicated in a variety of critical cellular functions, such as DNA repair and replication, RNA metabolism, and stress responses (8, 16, 20). Importantly, the SUMO system is highly dynamic and the SUMO pathway enzymes appear to work together to precisely control SUMO conjugate levels in the cell (8, 16, 20). However, how the SUMO system itself is regulated is poorly understood.Localization of the SUMO pathway enzymes may play an important role in SUMO system function (21). For example, the budding yeast SUMO protease Ulp1 is tethered to the nuclear face of the nuclear pore complex (NPC) via an unconventional interaction with the karyopherin Kap121 and the heterodimeric Kap95/Kap60 complex (12, 13, 23). However, this SUMO protease is not maintained exclusively at the NPC but appears to be mobile, effecting desumoylation at diverse subcellular locations: e.g., during mitosis, Saccharomyces cerevisiae Ulp1 is recruited to the septin ring to desumoylate septins (15), Schizosaccharomyces pombe Ulp1 localization is regulated throughout the cell cycle (31), and a mammalian Ulp1 homolog, SENP2, is shuttled between the nucleus and the cytoplasm (7). Consistent with these observations, SUMO conjugate levels are significantly altered in yeast strains expressing mislocalized Ulp1 (13, 37).Dramatic changes in SUMO conjugate populations have been noted in response to many different types of stresses in yeasts, mammals, and plants (9, 17, 27, 32, 38). For example, in S. cerevisiae, significantly increased steady-state SUMO conjugate levels are observed in response to elevated concentrations of ethanol (38). To better understand how the SUMO system is regulated in response to stress, we utilized alcohol as a model of a physiologically relevant stressor in yeast. Here, we demonstrate that alcohol stress results in a rapid, reversible nucleolar sequestration of Ulp1 and that enforced localization of Ulp1 in the nucleolus leads to a dramatic increase in steady-state SUMO conjugate levels. This is the first demonstration of regulated modulation of the intracellular localization of a SUMO enzyme in response to stress and thus represents a novel mechanism for SUMO system control.     

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

Background  

Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts.