Bernardgoldman0218

DNA-protein cross-links (DPCs) are unusually bulky DNA lesions that form when cellular proteins become trapped on DNA following exposure to ultraviolet light, free radicals, aldehydes, and transition metals. Selleck Dihydroethidium DPCs can also form endogenously when naturally occurring epigenetic marks [5-formyl cytosine (5fC)] in DNA react with lysine and arginine residues of histones to form Schiff base conjugates. Our previous studies revealed that DPCs inhibit DNA replication and transcription but can undergo proteolytic cleavage to produce smaller DNA-peptide conjugates. We have shown that 5fC-conjugated DNA-peptide cross-links (DpCs) placed within the CXA sequence (X = DpC) can be bypassed by human translesion synthesis (TLS) polymerases η and κ in an error-prone manner. However, the local nucleotide sequence context can have a strong effect on replication bypass of bulky lesions by influencing the geometry of the ternary complex among the DNA template, polymerase, and the incoming dNTP. In this work, we investigated polymerase bypass of 5fC-DNA-11-mer peptide cross-links placed in seven different sequence contexts (CXC, CXG, CXT, CXA, AXA, GXA, and TXA) in the presence of human TLS polymerase η. Primer extension products were analyzed by gel electrophoresis, and steady-state kinetics of the misincorporation of dAMP opposite the DpC lesion in different base sequence contexts was investigated. Our results revealed a strong impact of nearest neighbor base identity on polymerase η activity in the absence and presence of a DpC lesion. Molecular dynamics simulations were used to structurally explain the experimental findings. Our results suggest a possible role of local DNA sequence in promoting TLS-related mutational hot spots in the presence and absence of DpC lesions.Mass spectrometry (MS) is a powerful tool in chemical research and substance identification. For the computational modeling of electron ionization MS, we have developed the quantum-chemical electron ionization mass spectra (QCEIMS) program. Here, we present an extension of QCEIMS to calculate collision-induced dissociation (CID) spectra. The more general applicability is accounted for by the new name QCxMS, where "x" refers to EI or CID. To this end, fragmentation and rearrangement reactions are computed "on-the-fly" in Born-Oppenheimer molecular dynamics (MD) simulations with the semiempirical GFN2-xTB Hamiltonian, which provides an efficient quantum mechanical description of all elements up to Z = 86 (Rn). Through the explicit modeling of multicollision processes between precursor ions and neutral gas atoms as well as temperature-induced decomposition reactions, QCxMS provides detailed insight into the collision kinetics and fragmentation pathways. In combination with the CREST program to determine the preferential protonation sites, QCxMS becomes the first standalone MD-based program that can predict mass spectra based solely on molecular structures as input. We demonstrate this for six organic molecules with masses ranging from 159 to 296 Da, for which QCxMS yields CID spectra in reasonable agreement with experiments.Appropriate management approaches are needed to minimize the proliferation of antibiotic resistance genes (ARGs) in reclaimed water distribution systems (RWDSs). Six laboratory-scale RWDSs were operated over 3 years receiving influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. Shotgun metagenomic sequencing was applied toward comprehensive characterization of resistomes, focusing on total ARGs, ARG mobility, and specific ARGs of clinical concern. ARGs such as aadA, bacA, blaOXA, mphE, msrE, sul1, and sul2 were found to be particularly sensitive to varying RWDS conditions. BAC filtration with chlorination most effectively achieved and maintained the lowest levels of nearly all metagenomically derived antibiotic resistance indicators. However, BAC filtration or addition of residual disinfectants alone tended to increase these indicators. Biofilm and sediment compartments harbored ARGs in disinfected systems, presenting a concern for their release to bulk water. Relative and absolute abundances of most ARGs tended to decrease with water age (up to 5 days), with notable exceptions in BAC-filtered chloraminated and no residual systems. Superchlorination of unfiltered water especially raised concerns in terms of elevation of clinically relevant and mobile ARGs. This study revealed that BAC filtration and disinfection must be carefully coordinated in order to effectively mitigate ARG dissemination via RWDSs.Dielectric polymer capacitors are extensively applied in advanced electronics by virtue of their extremely high power density. However, it remains a challenge to concurrently realize high energy density and high discharge efficiency. In order to solve this conundrum, we herein design a novel all-polymer trilayer structure, where the paraelectric poly(methyl methacrylate) (PMMA) is used as the top layer to obtain a high discharge efficiency, and ferroelectric P(VDF-HFP) is employed as the bottom layer to obtain a high energy density. Particularly, the PMMA/poly(vinylidene fluoride-hexafluoropropylene) (P(VDF-HFP)) blend composite is used as the middle layer to homogenize the electric field inside the trilayer composites, turning out an obviously boosted breakdown strength and elevated energy density. Consequently, an efficiency as high as 85% and an energy density up to 7.5 J/cm3 along with excellent cycling stability are simultaneously realized at an ultrahigh electric field of 490 kV/mm. These attractive characteristics of the all-polymer trilayer structure suggest that the feasible pathway presented herein is significant to realize concurrently a high energy density and discharge efficiency.Tuberous sclerosis protein complex (pTSC) nucleates a proteinaceous signaling hub that integrates information about the internal and external energy status of the cell in the regulation of growth and energy consumption. Biochemical and cryo-electron microscopy studies of recombinant pTSC have revealed its structure and stoichiometry and hinted at the possibility that the complex may form large oligomers. Here, we have partially purified endogenous pTSC from fasted mammalian brains of rat and pig by leveraging a recombinant antigen binding fragment (Fab) specific for the TSC2 subunit of pTSC. We demonstrate Fab-dependent purification of pTSC from membrane-solubilized fractions of the brain homogenates. Negative stain electron microscopy of the samples purified from pig brain demonstrates rod-shaped protein particles with a width of 10 nm, a variable length as small as 40 nm, and a high degree of conformational flexibility. Larger filaments are evident with a similar 10 nm width and a ≤1 μm length in linear and weblike organizations prepared from pig brain.