INTACT proteomics in Xenopus

Analysis of the molecular mechanisms driving cell specification, differentiation, and other cellular processes can be difficult due to the heterogeneity of tissues and organs. Therefore, it is critical to isolate pure cell populations in order to properly assess the function of certain cell types in the context of a tissue. This protocol describes use of the INTACT (isolation of nuclei tagged in specific cell types) method in Xenopus, followed by proteomics analysis of nuclear protein complexes. The INTACT protocol utilizes two transgenes: (1) a three-part nuclear targeting fusion (NTF) consisting of a nuclear envelope protein (Nup35) that targets the NTF to the nuclear membrane, an enhanced green fluorescent protein (EGFP) cassette for NTF visualization in live animals, and a biotin ligase receptor protein (BLRP) that provides a substrate for the biotinylation of the NTF, and (2) the E. coli ligase BirA (which biotinylates the NTF) tagged to mCherry (for visualization). Either or both transgenes are driven by a tissue-specific promoter, making this protocol easily adaptable to proteomics analyses of immunoprecipitated complexes from INTACT-isolated nuclei of multiple tissue types to determine the composition of protein complexes in pure cell populations

Association between HindIII (rs320) variant in the lipoprotein lipase gene and the presence of coronary artery disease and stroke among the Saudi population

Lipoprotein Lipase (LPL) is known to be a key enzyme for lipid metabolism specifically in an enzymatic glycoprotein which provide tissues without fatty-acids and eliminates triglycerides (TG) by the circulation. Mutations in LPL were proven to cause alteration in fractions within lipoprotein, causing the development of atherosclerosis which predispose to weakening coronary artery disease (CAD) and stroke. We examined the linkage between genetic variant HindIII in LPL on lipoprotein fractions, stroke occurrences and CAD. In this case-control study, we have recruited 315 CAD cases and 205 age-matched controls. A total of 520 genomic DNA was digested with the purified PCR products for restriction fragment length polymorphism with HindIII restriction enzyme. The distribution of genotypes in a decreasing order were TT, 148 (47%), GT 135 (42.9%) and GG 32 (10.2%) in CAD groups of the study while the pattern in controls were GT 91 (44.4%), TT 86 (42%) and GG 28 (13.7%). None of all the allele or genotype frequencies were found to be significant in our study (p greater than 0.05), while the biochemical levels for both TG and LDL-c were shown to be prone in CAD patients when compare with the controls. Furthermore, the occurence of strokes were more in CAD groups vs. controls: 72 (22.9%) vs. 7 (3.4%) [p 0.000]. This could indicate the influence of HindIII variant on plasma lipid levels, and the possibility of considering it a risk factor for atherosclerosis leading to CAD and stroke occurrence

Economic crisis and the construction of a neo-liberal regulatory regime in Korea

A consistent theme of the literature on the ontology of the 1997 South Korean crisis is the key role played by regulatory failures and the growing weakness of the state. This paper seeks to briefly highlight both the insights and the limitations of this approach to understanding the crisis. Having done so, we shall set out the argument that the crisis created an opportunity for reformist Korean élites to advance their longstanding, but previously frustrated, project to create a comprehensive unambiguously neo-liberal regulatory regime. This paper will also seek to highlight the implications of our reading of the development of the Korean political economy for broader debates on economic liberalisation, crisis and the future of the developmental state

A genetic variant c.553G > T (rs2075291) in the apolipoprotein A5 gene is associated with altered triglycerides levels in coronary artery disease (CAD) patients with lipid lowering drug

Background: Elevated plasma triglycerides (TGs) are widely used as a major cardiovascular risk predictor and are thought to play an important role in the progression of coronary heart disease (CHD). It has been demonstrated that lipid lowering was associated with lower mortality in patients with CHD. The present study therefore aimed to investigate the consequences of the genetic variant c.553G>T (rs2075291) in apolipoprotein A5 gene to determination of triglycerides levels in CAD patients receiving, atorvastatin, lipid lowering drug. Methods: We here report that a recently identified genetic variant, c.553G>T in the APOA5 gene which causes a substitution of a cysteine for a glycine residue at amino acid residue 185(G185C) is also associated with increased TG levels. To investigate theses effects, a case-control study compressing 608 subjects from the same area was performed.ResultsTG levels in T allele patients were significantly lower than the control GT allele patient ((2)=2.382E2(a), P-value T variant (rs2075291); in APOA5 gene increases human plasma TG levels. Conclusion: Nevertheless, T allele is found to reduce TG levels in CAD patients who are on the cholesterol medication, atorvastatin. Thus, c.553G>T variant can be considered as a significant predicator of hypertriglyceridemia. In addition, it could be used as a hallmark for the diagnosis and prognosis of CAD

Human liver memory CD8(+) T cells use autophagy for tissue residence

Tissue-resident memory T cells have critical roles in long-term pathogen and tumor immune surveillance in the liver. We investigate the role of autophagy in equipping human memory T cells to acquire tissue residence and maintain functionality in the immunosuppressive liver environment. By performing ex vivo staining of freshly isolated cells from human liver tissue, we find that an increased rate of basal autophagy is a hallmark of intrahepatic lymphocytes, particularly liver-resident CD8(+) T cells. CD8(+) T cells with increased autophagy are those best able to proliferate and mediate cytotoxicity and cytokine production. Conversely, blocking autophagy induction results in the accumulation of depolarized mitochondria, a feature of exhausted T cells. Primary hepatic stellate cells or the prototypic hepatic cytokine interleukin (IL)-15 induce autophagy in parallel with tissue-homing/retention markers. Inhibition of T cell autophagy abrogates tissue-residence programming. Thus, upregulation of autophagy adapts CD8(+) T cells to combat mitochondrial depolarization, optimize functionality, and acquire tissue residence

EV-scale sterile neutrino search using eight years of atmospheric muon neutrino data from the IceCube Neutrino Observatory

The results of a 3+1 sterile neutrino search using eight years of data from the IceCube Neutrino Observatory are presented. A total of 305 735 muon neutrino events are analyzed in reconstructed energy-zenith space to test for signatures of a matter-enhanced oscillation that would occur given a sterile neutrino state with a mass-squared differences between 0.01 and 100  eV². The best-fit point is found to be at sin²(2θ₂₄)=0.10 and Δm²₄₁=4.5  eV², which is consistent with the no sterile neutrino hypothesis with a p value of 8.0%.M.G. Aartsen … G.H. Collin … G.C. Hill … A. Kyriacou … A. Wallace … B.J. Whelan … et al. (The IceCube Collaboration

Search for Correlations of High-energy Neutrinos Detected in IceCube with Radio-bright AGN and Gamma-Ray Emission from Blazars

Published 2023 August 23The IceCube Neutrino Observatory sends realtime neutrino alerts with a high probability of being astrophysical in origin. We present a new method to correlate these events and possible candidate sources using 2089 blazars from the Fermi-LAT 4LAC-DR2 catalog and with 3413 active galactic nuclei (AGNs) from the Radio Fundamental Catalog. No statistically significant neutrino emission was found in any of the catalog searches. The result suggests that a small fraction, <1%, of the studied AGNs emit neutrinos that pass the alert criteria, and is compatible with prior evidence for neutrino emission presented by IceCube and other authors from sources such as TXS 0506 + 056 and PKS 1502 + 106. We also present cross-checks to other analyses that claim a significant correlation using similar data samples.R. Abbasi ... R. T. Burley ... E. G. Carnie-Bronca ... G. H. Collin ... G. C. Hill ... E. J. Roberts ... et al. (IceCube Collaboration

Graph Neural Networks for low-energy event classification & reconstruction in IceCube

Published: November 4, 2022IceCube, a cubic-kilometer array of optical sensors built to detect atmospheric and astrophysical neutrinos between 1 GeV and 1 PeV, is deployed 1.45 km to 2.45 km below the surface of the ice sheet at the South Pole. The classification and reconstruction of events from the in-ice detectors play a central role in the analysis of data from IceCube. Reconstructing and classifying events is a challenge due to the irregular detector geometry, inhomogeneous scattering and absorption of light in the ice and, below 100 GeV, the relatively low number of signal photons produced per event. To address this challenge, it is possible to represent IceCube events as point cloud graphs and use a Graph Neural Network (GNN) as the classification and reconstruction method. The GNN is capable of distinguishing neutrino events from cosmic-ray backgrounds, classifying different neutrino event types, and reconstructing the deposited energy, direction and interaction vertex. Based on simulation, we provide a comparison in the 1 GeV–100 GeV energy range to the current state-of-the-art maximum likelihood techniques used in current IceCube analyses, including the effects of known systematic uncertainties. For neutrino event classification, the GNN increases the signal efficiency by 18% at a fixed background rate, compared to current IceCube methods. Alternatively, the GNN offers a reduction of the background (i.e. false positive) rate by over a factor 8 (to below half a percent) at a fixed signal efficiency. For the reconstruction of energy, direction, and interaction vertex, the resolution improves by an average of 13%–20% compared to current maximum likelihood techniques in the energy range of 1 GeV–30 GeV. The GNN, when run on a GPU, is capable of processing IceCube events at a rate nearly double of the median IceCube trigger rate of 2.7 kHz, which opens the possibility of using low energy neutrinos in online searches for transient events.R. Abbasi ... R.T. Burley ... E.G. Carnie-Bronca ... G.H. Collin ... G.C. Hill ... E.J. Roberts ... et al. (The IceCube collaboration