A scrapie-like unfolding intermediate of the prion protein domain PrP(121-231) induced by acidic pH

The infectious agent of transmissible spongiform encephalopathies is believed to consist of an oligomeric isoform, PrPSc, of the monomeric cellular prion protein, PrPC. The conversion of PrPC to PrPSc is characterized by a decrease in alpha-helical structure, an increase in beta-sheet content, and the formation of PrPSc amyloid. Whereas the N-terminal part of PrPC comprising residues 23-120 is flexibly disordered, its C-terminal part, PrP(121-231), forms a globular domain with three alpha-helices and a small beta-sheet. Because the segment of residues 90-231 is protease-resistant in PrPSc, it is most likely structured in the PrPSc form. The conformational change of the segment containing residues 90-120 thus constitutes the minimal structural difference between PrPC and a PrPSc monomer. To test whether PrP(121-231) is also capable to undergo conformational transitions, we analyzed its urea-dependent unfolding transitions at neutral and acidic pH. We identified an equilibrium unfolding intermediate of PrP(121-231) that is exclusively populated at acidic pH and shows spectral characteristics of a beta-sheet protein. The intermediate is in rapid equilibrium with native PrP(121-231), significantly populated in the absence of urea at pH 4.0, and may have important implications for the presumed formation of PrPSc during endocytosis

Shock recovery experiments confirm the possibility of transferring viable microorganisms from Mars to Earth

Extract from introduction: With regard to the impact and ejection phase we tested the case for the transfer of microorganisms from Mars to Earth. Using a high explosive set-up thin layers of bacterial endospores of Bacillus subtilis, of the lichen Xanthoria elegans and of the cyanobacterium Chroococcidiopsis sp. embedded between two plates of gabbro were subjected to 10, 20, 30, 40 and 50 GPa which is the pressure range observed in Martian meteorites [1]

Life after shock: the mission from Mars to Earth

Extract from introduction: The minerals of the Martian meteorites collected so far indicate an exposure to shock waves in the pressure range of 5 to 55 GPa [1]. As terrestrial rocks are frequently inhabited by microbial communities, rocks ejected from a planet by impact processes may carry with them endolithic microorganisms, if microbial life existed/exists on this planet

Impact experiments in support of “Lithopanspermia”: The route from Mars to Earth

Shock recovery experiments on a Martian analogue rock (gabbro) loaded with three types of microorganisms reveal that these organisms survive the impact and ejection phase on Mars at shock pressures up to about 50 GPa with exponentially decreasing survival rates

The influence of shock pressure, pre-shock temperature, and host rock composition on the survival rate of endolithic microorganisms during impact ejection from Mars

Petrographic and biological analysis of shock recovery experiments confirms the possible life transport due to an impact from Mars to Earth

Altered sphingoid base profiles in type 1 compared to type 2 diabetes

Background: Sphingolipids are increasingly recognized to play a role in insulin resistance and diabetes. Recently we reported significant elevations of 1-deoxysphingolipids (1-deoxySL) - an atypical class of sphingolipids in patients with metabolic syndrome (MetS) and diabetes type 2 (T2DM). It is unknown whether 1-deoxySL in patients with diabetes type 1 (T1DM) are similarly elevated. Findings: We analyzed the long chain base profile by LC-MS after hydrolyzing the N-acyl and O-linked headgroups in plasma from individuals with T1DM (N = 27), T2DM (N = 30) and healthy controls (N = 23). 1-deoxySLs were significantly higher in the groups with T2DM but not different between T1DM and controls. In contrast to patients with T2DM, 1-deoxSL levels are not elevated in T1DM. Conclusions: Our study indicates that the 1-deoxySL formation is not per-se caused by hyperglycemia but rather specifically associated with metabolic changes in T2DM, such as elevated triglyceride levels. Electronic supplementary material The online version of this article (doi:10.1186/1476-511X-13-161) contains supplementary material, which is available to authorized users

Hepatocyte ABCA1 deficiency is associated with reduced HDL sphingolipids

ATP binding cassette transporter A1 (ABCA1) limits the formation of high density lipoproteins (HDL) as genetic loss of ABCA1 function causes virtual HDL deficiency in patients with Tangier disease. Mice with a hepatocyte-specific ABCA1 knockout (Abca1 HSKO) have 20% of wild type (WT) plasma HDL-cholesterol levels, suggesting a major contribution of hepatic ABCA1 to the HDL phenotype. Whether plasma sphingolipids are reduced in Tangier disease and to what extent hepatic ABCA1 contributes to plasma sphingolipid (SL) levels is unknown. Here, we report a drastic reduction of total SL levels in plasma of a Tangier patient with compound heterozygosity for mutations in ABCA1. Compared to mutation-free controls, heterozygous mutations in ABCA1 had no significant effect on total SLs in plasma; however, apoB-depleted plasma showed a reduction in total SL also in het carriers. Similarly, liver specific Abca1 KO mice (Abca1 HSKO) showed reduced total sphingolipids in plasma and liver. In parallel, apoM and sphingosine-1-phosphate (S1P) levels were reduced in plasma of Abca1 HSKO mice. Primary hepatocytes from Abca1 HSKO mice showed a modest, but significant reduction in total SLs concentration compared to WT hepatocytes, although SL de novo synthesis and secretion were slightly increased in Abca1 HSKO hepatocytes. We conclude that hepatic ABCA1 is a signficant contributor to maintaining total plasma pool of HDL sphingolipids, including sphingomyelins and S1P

Compressed AFM-IR hyperspectral nanoimaging

Infrared (IR) hyperspectral imaging is a powerful approach in the field of materials and life sciences. However, for the extension to modern sub-diffraction nanoimaging it still remains a highly inefficient technique, as it acquires data via inherent sequential schemes. Here, we introduce the mathematical technique of low-rank matrix reconstruction to the sub-diffraction scheme of atomic force microscopy-based infrared spectroscopy (AFM-IR), for efficient hyperspectral IR nanoimaging. To demonstrate its application potential, we chose the trypanosomatid unicellular parasites Leishmania species as a realistic target of biological importance. The mid-IR spectral fingerprint window covering the spectral range from 1300 to 1900 cm−1 was chosen and a distance between the data points of 220 nm was used for nanoimaging of single parasites. The method of k-means cluster analysis was used for extracting the chemically distinct spatial locations. Subsequently, we randomly selected only 10% of an originally gathered data cube of 134 (x) × 50 (y) × 148 (spectral) AFM-IR measurements and completed the full data set by low-rank matrix reconstruction. This approach shows agreement in the cluster regions between full and reconstructed data cubes. Furthermore, we show that the results of the low-rank reconstruction are superior compared to alternative interpolation techniques in terms of error-metrics, cluster quality, and spectral interpretation for various subsampling ratios. We conclude that by using low-rank matrix reconstruction the data acquisition time can be reduced from more than 14 h to 1–2 h. These findings can significantly boost the practical applicability of hyperspectral nanoimaging in both academic and industrial settings involving nano- and bio-materials

Effects of diets high in animal or plant protein on oxidative stress in individuals with type 2 diabetes: a randomized clinical trial

High-protein diet is a promising strategy for diabetes treatment supporting body weight control, improving glycaemic status, cardiovascular risk factors and reducing liver fat. Here, we investigated effects of diets high in animal (AP) or plant (PP) protein on oxidative stress and antioxidant status in individuals with type 2 diabetes (T2DM). 37 obese individuals (age 64.3 ± 1.0 years) with T2DM were randomized to an isocaloric diet (30 energy(E)% protein, 30E% fat and 40E% carbohydrates) rich in AP or PP for 6 weeks. Markers of oxidative and nitrosative stress and antioxidant status in plasma and nitrate/nitrite levels in urine were assessed. Gene expression in subcutaneous adipose tissue (SAT) was analyzed by RNA-Seq and real-time PCR.Both AP and PP diets similarly reduced plasma levels of malondialdehyde (P(AP) = 0.003, P(PP) = 1.6x10(-4)) and protein carbonyls (P(AP) = 1.2x10(-4), P(PP) = 3.0x10(-5)) over 6 weeks. Nitrotyrosine (NT) increased upon both AP and PP diets (PAP = 0.005,PPP = 0.004). SAT expression of genes involved in nitric oxide (NO) and oxidative stress metabolism and urine NO metabolite (nitrate/nitrite) levels were not changed upon both diets. Plasma levels of carotenoids increased upon PP diet, whereas retinol, alpha- and gamma-tocopherol slightly decreased upon both diets. AP and PP diets similarly improve oxidative stress but increase nitrosative stress markers in individuals with T2DM. Mechanisms of the NT regulation upon high-protein diets need further investigation

Novel regulators of PrPC biosynthesis revealed by genome-wide RNA interference

The cellular prion protein PrPC is necessary for prion replication, and its reduction greatly increases life expectancy in animal models of prion infection. Hence the factors controlling the levels of PrPC may represent therapeutic targets against human prion diseases. Here we performed an arrayed whole-transcriptome RNA interference screen to identify modulators of PrPC expression. We cultured human U251-MG glioblastoma cells in the presence of 64'752 unique siRNAs targeting 21'584 annotated human genes, and measured PrPC using a one-pot fluorescence-resonance energy transfer immunoassay in 51'128 individual microplate wells. This screen yielded 743 candidate regulators of PrPC. When downregulated, 563 of these candidates reduced and 180 enhanced PrPC expression. Recursive candidate attrition through multiple secondary screens yielded 54 novel regulators of PrPC, 9 of which were confirmed by CRISPR interference as robust regulators of PrPC biosynthesis and degradation. The phenotypes of 6 of the 9 candidates were inverted in response to transcriptional activation using CRISPRa. The RNA-binding post-transcriptional repressor Pumilio-1 was identified as a potent limiter of PrPC expression through the degradation of PRNP mRNA. Because of its hypothesis-free design, this comprehensive genetic-perturbation screen delivers an unbiased landscape of the genes regulating PrPC levels in cells, most of which were unanticipated, and some of which may be amenable to pharmacological targeting in the context of antiprion therapies