Neuroprotective Effects of Heat-Killed Lactobacillus plantarum 200655 Isolated from Kimchi Against Oxidative Stress

Probiotics and Antimicrobial Proteins - Oxidative stress plays an important role in exacerbating neurodegenerative diseases, such as Alzheimer's disease, Parkinson’s disease, and...     

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side

Background

Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. The genome information exchange between the patient and the hospital has become more popular. However, the genome sequence information is innate and irreversible and thus its leakage has serious consequences. Therefore, protecting one’s genome information is critical. On the other side, hospitals may need to protect their own panels. There is no known secure SNP panel scheme to protect both.

Results

In this paper, we propose a secure SNP panel scheme using homomorphically encrypted K-mers without requiring SNP calling on the user side and without revealing the panel information to the user. Use of the powerful homomorphic encryption technique is desirable, but there is no known algorithm to efficiently align two homomorphically encrypted sequences. Thus, we designed and implemented a novel secure SNP panel scheme utilizing the computationally feasible equality test on two homomorphically encrypted K-mers. To make the scheme work correctly, in addition to SNPs in the panel, sequence variations at the population level should be addressed. We designed a concept of Point Deviation Tolerance (PDT) level to address the false positives and false negatives. Using the TCGA BRCA dataset, we demonstrated that our scheme works at the level of over a hundred thousand somatic mutations. In addition, we provide a computational guideline for the panel design, including the size of K-mer and the number of SNPs.

Conclusions

The proposed method is the first of its kind to protect both the user’s sequence and the hospital’s panel information using the powerful homomorphic encryption scheme. We demonstrated that the scheme works with a simulated dataset and the TCGA BRCA dataset. In this study, we have shown only the feasibility of the proposed scheme and much more efforts should be done to make the scheme usable for clinical use.

     

Activation of AMP-activated protein kinase mediates acute and severe hypoxic injury to pancreatic beta cells

In islet transplantation, a substantial part of the graft becomes nonfunctional for several reasons including hypoxia. AMP-activated protein kinase (AMPK) in mammalian cells is a regulator of energy homeostasis, and is activated by metabolic stresses such as hypoxia. However, the role of AMPK in hypoxic injury to pancreatic beta cells is not clear. When a rat beta cell line, INS-1 cell, was incubated in an anoxic chamber, phosphorylation of both AMPK and its downstream protein, acetyl-CoA carboxylase 2 increased with time. Adenovirus-mediated expression of constitutively active form of AMPK under normoxic conditions increased caspase-3 activation, suggesting induction of apoptosis. Reactive oxygen species production also increased with time during hypoxia. Pretreatment with compound C, an AMPK inhibitor, or N-acetyl-l-cysteine, an antioxidant, significantly lowered hypoxia-mediated cell death. These results suggest that AMPK, in association with oxidative stress, plays an important role in acute and severe hypoxic injury to pancreatic beta cells.     

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson''s. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17–42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17–42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer’s disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular.     

Impact of sequence on the molecular assembly of short amyloid peptides

The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48‐peptide systems containing SNQNNF ( PrP (170–175 )), SSTSAA (RNaseA(15–20)), MVGGVV (Aβ(35–40)), GGVVIA (Aβ(37–42)), and MVGGVVIA (Aβ(35–42)). In our simulations SNQQNF, SSTTSAA, and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β‐sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C‐terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1–42) assembles into more complex oligomers than Aβ(1–40), a consequence of which is that it is more strongly associated with Alzheimer's disease. Proteins 2014; 82:1469–1483. © 2014 Wiley Periodicals, Inc.     

Efficient Itaconic acid production via protein–protein scaffold introduction between GltA,AcnA, and CadA in recombinant Escherichia coli

Itaconic acid, which is a promising organic acid in synthetic polymers and some base-material production, has been produced by Aspergillus terreus fermentation at a high cost. The recombinant Escherichia coli that contained the cadA gene from A. terreus can produce itaconic acid but with low yield. By introducing the protein–protein scaffold between citrate synthesis, aconitase, and cis-aconitase decarboxylase, 5.7 g/L of itaconic acid was produced, which is 3.8-fold higher than that obtained with the strain without scaffold. The optimum pH and temperature for itaconic acid production were 8.5 and 30°C, respectively. When the competing metabolic network was inactivated by knock-out mutation, the itaconic acid concentration further increased, to 6.57 g/L.     

Extraction of lactic acid with colloidal liquid aphrons and comparison of their toxicities with solvents without surfactant on the viability of Lactobacillus rhamnosus

Colloidal liquid aphrons (CLAs) are surfactant-stabilized solvent droplets which have recently been explored for predispersed solvent extraction (PDSE). We have compared the equilibrium distribution of lactic acid with solvent alone and with CLAs. In spite of the short contact time in the PDSE process with CLAs, there was little difference in equilibrium distribution with solvent alone. The toxicity of extractants and diluents on Lactobacillus rhamnosus was measured for in situ extraction. Long chain alcohols such as 1-octanol and 1-decanol were less toxic among diluents. CLAs reduced the toxicity of solvents on Lactobacillus rhamnosus.