Self-Organized Criticality in Protein Folding Simulations with AMBER Parameters

AMBER (Assisted Model Building with Energy Refinement) is a force field that allows for the simulation of proteins. Basic proteins were folded by a Monte-Carlo algorithm parameterized by AMBER on MATLAB. Simulations exhibited self-organized critical (SOC) behavior and are shown to be stable throughout the simulations by use of pairwise distance matrixes. Frequency shifting is explored as a possible explanation of the mechanisms behind structure inducing probes (SIPs) in the solid phase synthesis of proteins. This also provides a mechanistic link to many other SOC systems

Physical Vapor Growth of Rubrene

Rubrene is a novel organic semiconductor, with many interesting electronic properties. Among organic semiconductors, rubrene has the highest carrier mobility, with values reaching 40 cm2/(V S). These electronic properties, however, are only applicable for crystallized and pure forms of rubrene. Physical vapor transport of rubrene is capable of purifying and crystallizing rubrene powder. This is accomplished by heating the impure sample and subjecting the sublimated vapors with a constant flow of Ar gas along a temperature gradient. We report efforts to build and test a physical vapor growth system for rubrene

Does a Simple Lattice Protein Folding Model Exhibit Self-Organized Criticality?

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the way they consistently fold to the same structure is unknown. Our research sees if the folding process can be viewed computationally through the lens of self-organized criticality using a simple lattice-bound protein

Mycophenolate mofetil as an alternative treatment for autoimmune hepatitis

Autoimmune hepatitis (AIH) is an immune-mediated chronic liver disease characterized by hepatocellular inflammation, necrosis, and fibrosis, which can progress to cirrhosis and fulminant hepatic failure. The standard treatment for AIH includes corticosteroids alone or in combination with azathioprine. Although most patients achieve remission using the standard regimen, some patients do not respond due to either drug intolerance or refractory disease; in such cases alternative immunosuppressive agents should be explored. The second-line therapies are cyclophilin inhibitors such as cyclosporine A or tacrolimus, and nowadays mycophenolate mofetil (MMF) is widely used if azathioprine-based therapies are not tolerated. Although these are recommended as an alternative to the first-line regimen, there is insufficient evidence for the efficacy of second-line therapies, with the evidence based mainly on expert opinion. Therefore, we report an AIH patient receiving the standard regimen in whom remission did not occur due to side effects to azathioprine, but was successfully treated with MMF in combination with corticosteroids as an alternative to the standard regimen

False-negative errors in next-generation sequencing contribute substantially to inconsistency of mutation databases.

BackgroundMore than 11,000 laboratories and companies developed their own next-generation sequencing (NGS) for screening and diagnosis of various diseases including cancer. Although inconsistencies of mutation calls as high as 43% in databases such as GDSC (Genomics of Drug Sensitivity in Cancer) and CCLE (Cancer Cell Line Encyclopedia) have been reported, not many studies on the reasons for the inconsistencies have been published. Methods: Targeted-NGS analysis of 151 genes in 35 cell lines common to GDSC and CCLE was performed, and the results were compared with those from GDSC and CCLE wherein whole-exome- or highly-multiplex NGS were employed.ResultsIn the comparison, GDSC and CCLE had a high rate (40-45%) of false-negative (FN) errors which would lead to high rate of inconsistent mutation calls, suggesting that highly-multiplex NGS may have high rate of FN errors. We also posited the possibility that targeted NGS, especially for the detection of low-level cancer cells in cancer tissues might suffer significant FN errors.ConclusionFN errors may be the most important errors in NGS testing for cancer; their evaluation in laboratory-developed NGS tests is needed

Cancer cells undergoing epigenetic transition show short-term resistance and are transformed into cells with medium-term resistance by drug treatment

Cancer chemotherapy: treatment prolongs resistance caused by DNA modification Cancer cells that are transiently resistant to drug therapies owing to changes in their gene expression patterns can become resistant for longer durations if exposed to the drug treatments. A team led by Kyeong-Man Hong and Hyonchol Jang from the National Cancer Center in Goyang, South Korea, used cellular reprogramming technologies to induce changes in the DNA markers that regulate gene expression. Working with lung and gastric cancer cell lines, the researchers found that such epigenetic alterations caused many cells to become resistant to the chemotherapy drugs cisplatin and paclitaxel. In the absence of treatment, the cells soon lost their drug resistance. In the presence of the chemotherapeutics, however, the resistance trait lasted longer, a finding that could inform best practice for how to administer cancer-fighting agents in the face of epigenetic-driven drug resistance