Lipidomic Analysis of α-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment

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Exploring Calbindin-IMPase fusion proteins structure and activity

Calbindin-D28k is a calcium binding protein that is highly expressed in the mammalian central nervous system. It has been reported that calbindin-D28k binds to and increases the activity of inositol Monophosphatase (IMPase). This is an enzyme that is involved in the homeostasis of the Inositol trisphosphate signalling cascade by catalysing the final dephosphorylation of inositol and has been implicated in the therapeutic mechanism of lithium treatment of bipolar disorder. Previously studies have shown that calbindin-D28k can increase IMPase activity by up to 250 hundred-fold. A preliminary in silico model was proposed for the interaction.Here, we aimed at exploring the shape and properties of the calbindin-IMPase complex to gain new insights on this biologically important interaction. We created several fusion constructs of calbindin-D28k and IMPase, connected by flexible amino acid linkers of different lengths and orientations to fuse the termini of the two proteins together. The resulting fusion proteins have activities 200%–400% higher the isolated wild-type IMPase. The constructs were characterized by small angle X-ray scattering to gain information on the overall shape of the complexes and validate the previous model. The fusion proteins form a V-shaped, elongated and less compact complex as compared to the model. Our results shed new light into this protein-protein interaction.     

Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I

Viruses are the most abundant biological entities in aquatic environments, typically exceeding the abundance of bacteria by an order of magnitude. The reliable enumeration of virus-like particles in marine microbiological investigations is a key measurement parameter. Although the size of typical marine viruses (20-200 nm) is too small to permit the resolution of details by light microscopy, such viruses can be visualized by epifluorescence microscopy if stained brightly. This can be achieved using the sensitive DNA dye SYBR Green I (Molecular Probes-Invitrogen). The method relies on simple vacuum filtration to capture viruses on a 0.02-microm aluminum oxide filter, and subsequent staining and mounting to prepare slides. Virus-like particles are brightly stained and easily observed for enumeration, and prokaryotic cells can easily be counted on the same slides. The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously.     

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of confident peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic Saccharomyces cerevisiae dataset, and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach.     

Population trends for humpback whales (Megaptera novaeangliae) foraging in the Francisco Coloane Coastal‐Marine Protected Area,Magellan Strait,Chile

In 2003 a feeding aggregation of southeastern Pacific humpback whales (Megaptera novaeangliae) was reported in the Magellan Strait. While Chile established its first marine national park in the Strait to protect humpback whale habitat, fatal ship strikes remain a concern because of overlap with a busy shipping lane. To better understand population risk, we estimated abundance and survival for this population using Bayesian robust‐design mark‐recapture models fit to photographic data from 2004 to 2016. Overall, the model estimated a total of 204 whales (95% CI: 199–210) during the last 12 yr, and 93 (95% CI: 86–100) in the 2016/2017 austral summer. The population grew at 2.3% (CI: 2.1%–3.1%), an annual increase of two whales. Annual survival (including calves) was estimated at 0.892 (CI: 0.871–0.910). Our results corroborate a persistent feeding population, but one that is increasing relatively slowly. Owing to its vulnerability stemming from its small size, coupled with significant overlap with a busy shipping lane, we argue this subpopulation is at significant risk from ship strikes and may be one of the few populations where anthropogenic mortalities could regulate population dynamics. We therefore encourage continued monitoring via photographic mark‐resighting surveys, and analyses explicitly investigating potential population‐level ship strike effects.     

Electrophoretic separation of plasma lipoproteins in agarose gel

A method has been developed for the separation of serum or plasma lipoproteins by electrophoresis in an agarose-agar gel mixture. The gel is applied to the surface of a thin polyester photographic film strip. With minor alterations in technique either single samples on individual strips or many samples on one large sheet may be processed. After fixation and dehydration the transparent film is stained with Sudan Black B and washed with water. The finished electrophoretogram can be obtained in 5 hr and consists of widely separated bands of lipoprotein fractions on a colorless transparent background, ideally suited for scanning with a densitometer. Plasma samples from different subjects show pre-beta lipoproteins of different mobilities. An effect of gel concentration on the extent of lipoprotein migration is demonstrated. The clearcut separation of lipoproteins by this method will facilitate the classification of hyperlipoproteinemias and improve quantitative estimates of lipoprotein distribution.     

Postmortem biochemical indices of antemortem hemorrhagic shock

The purpose of this study was to determine if the perturbations in two glycolytic metabolites that occur during hemorrhagic shock can be used as discriminatory postmortem indicators of death resulting from severe hemorrhagic shock. Two groups of male albino Sprague-Dawley rats were hemorrhaged by withdrawing either 40% (Group I) or 45% (Group II) of the total blood volume. Glycogen and lactate concentrations were determined at 0 and 48 hr postmortem in the following tissues and organs: diaphragm, heart, liver, kidney cortex, and kidney medulla. The differences in lactate and glycogen in Group I at 0 hr were not significantly different from the nonhemorrhaged controls, with the exception of the lower liver glycogen concentration (58% of control). In Group II glycogen concentration was significantly reduced at 0 hr in the diaphragm (70% of control), liver (37%), and kidney medulla (55%). Lactate concentration was higher in all tissues examined by 270-640%; within 48 hr all tissues for both control and hemorrhaged animals had declined to baseline levels of glycogen concentration, whereas lactate levels had increased as much as 34-fold. There were no highly significant differences in glycogen at 48 hr between the control and hemorrhaged groups. In Group II the lactates were similar for both the control and hemorrhaged animals with the exception of the higher concentrations in the kidney cortex (54%) and medulla (41%). It was concluded from these findings that although significant metabolic perturbations are present at the time of death due to hemorrhage these differences do not persist up to 48 hr postmortem, with the possible exception of the kidney lactate concentrations.     

Factor interactions with the simian virus 40 early pre-mRNA influence branch site selection and alternative splicing.

To study the interaction of splicing factors with the simian virus 40 early-region pre-RNA, which can be alternatively spliced to produce large T and small t mRNAs, we used an in vitro RNase protection assay that defines the 5' boundaries of factor-RNA interactions. Protection products reflecting factor interactions with the large T and small t 5' splice sites and with the multiple lariat branch site region were characterized. All protection products were detected very early in the splicing reaction, before the appearance of spliced RNAs. However, protection of the large T 5' splice site was detected well before small t 5' splice site and branch site protection products, which appeared simultaneously. Oligonucleotide-targeted degradation of small nuclear RNAs (snRNAs) revealed that protection of the branch site region, which occurred at multiple sites, required intact U2 snRNA and was enhanced by U1 snRNA, while protection of the large T and small t 5' splice sites required both U1 and U2 snRNAs. Analysis of several pre-RNAs containing mutations in the branch site region suggests that factor interactions involving the multiple copies of the branch site consensus determine the selection of branch points, which is an important factor in the selection of alternative splicing pathways.