Purpose: This study aimed to establish a nomogram combining 31-gene signature (31-GS), radiosensitivity index (RSI), and radiation-resistance-related gene index (RRRI) to predict recurrence in prostate cancer (PCa) patients.
Methods And Materials: Transcriptome data of PCa were obtained from gene expression omnibus and the cancer genome atlas to validate the predictive potential of 3 sets of published biomarkers, namely, 31-GS, RSI, and RRRI. To adjust these markers for the characteristics of PCa, we analyzed 4 PCa-associated radiosensitivity predictive indices based on 31-GS, RSI, and RRRI by the Cox analysis and least absolute shrinkage and selection operator regression analysis.
Native mass spectrometry (nMS) is an increasingly popular technique for studying intact protein quaternary structure. When coupled with ion mobility, which separates ions based on their size, charge, and shape, it provides additional structural information on the protein complex of interest. We present here data from a novel prototype TIMS (trapped ion mobility spectrometry)-quadrupole-SID (surface-induced dissociation)-time of flight, TIMS-Q-SID-TOF, instrument for nMS.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
July 2024
Mass-spectrometry based assays in structural biology studies measure either intact or digested proteins. Typically, different mass spectrometers are dedicated for such measurements: those optimized for rapid analysis of peptides or those designed for high molecular weight analysis. A commercial trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) platform is widely utilized for proteomics and metabolomics, with ion mobility providing a separation dimension in addition to liquid chromatography.
View Article and Find Full Text PDFMonocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots.
View Article and Find Full Text PDFThe assembly of the β-amyloid peptide (Aβ) to form oligomers and fibrils is closely associated with the pathogenesis and progression of Alzheimer's disease. Aβ is a shape-shifting peptide capable of adopting many conformations and folds within the multitude of oligomers and fibrils the peptide forms. These properties have precluded detailed structural elucidation and biological characterization of homogeneous, well-defined Aβ oligomers.
View Article and Find Full Text PDFAβ oligomers play a central role in the neurodegeneration observed with Alzheimer's disease. Our laboratory has developed covalently stabilized trimers derived from residues 17-36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells.
View Article and Find Full Text PDFTo improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage.
View Article and Find Full Text PDFWe describe the implementation of a simple three-electrode surface-induced dissociation (SID) cell on a cyclic ion mobility spectrometer (cIMS) and demonstrate the utility of multipass mobility separations for resolving multiple conformations of protein complexes generated during collision-induced and surface-induced unfolding (CIU & SIU) experiments. In addition to CIU and SIU, SID of protein complexes is readily accomplished within the native instrument software and with no additional external power supplies by entering a single SID collision energy, a simplification in user experience compared to prior implementations. A set of cyclic homomeric protein complexes and a heterohexamer with known CID and SID behavior were analyzed to investigate mass and mobility resolution improvements, the latter of which improved by 20-50% (median: 33%) compared to a linear travelling wave device.
View Article and Find Full Text PDFWe describe instrumentation for conducting tandem surface-induced dissociation (tSID) of native protein complexes on an ultrahigh resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The two stages of SID are accomplished with split lenses replacing the entrance lenses of the quadrupole mass filter (stage 1, referred to herein as SID-Q) and the collision cell (stage 2, Q-SID). After SID-Q, the scattered projectile ions and subcomplexes formed in transit traverse the 20 mm pre-filter prior to the mass-selecting quadrupole, providing preliminary insights into the SID fragmentation kinetics of noncovalent protein complexes.
View Article and Find Full Text PDFMachining temperature is a key factor in ultrasonic vibration-assisted milling as it can significantly influence tool wear rate and residual thermal stresses. In current study, a physics-based analytical predictive model on machining temperature in ultrasonic vibration-assisted milling is proposed, without resorting to iterative numerical simulations. As the tool periodically loses contact with the workpiece under vibration, three types of tool-workpiece separation criteria are first examined based on the tool trajectory under ultrasonic vibration.
View Article and Find Full Text PDFZinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g.
View Article and Find Full Text PDFAbnormalities in zinc metabolism have been linked to many diseases, including different kinds of cancers and neurological diseases. The present study investigates the fragmentation pathways of a zinc chaperon using a model peptide with the sequence acetyl-His-Cys-Gly-Pro-Tyr-His-Cys (analog methanobactin peptide-5, amb). DFT/M05-2X and B3LYP geometry optimizations of [amb-3H+Zn(II)] predicted three lowest energy conformers with different chelating motifs.
View Article and Find Full Text PDFTEOSINTE-BRANCHED/CYCLOIDEA/PCF (TCP) proteins are plant-specific transcription factors known to have a role in multiple aspects of plant growth and development at the cellular, organ and tissue levels. However, there has been no related study of TCPs in orchids. Here we identified 23 TCP genes from the genome sequence of Phalaenopsis equestris Phylogenetic analysis distinguished two homology classes of PeTCP transcription factor families: classes I and II.
View Article and Find Full Text PDF2-(3-Methoxyphenyl)-5-methyl-1,8-naphthyridin-4(1H)-one (HKL-1), a 2-phenyl-1,8-naphthyridin-4-one (2-PN) derivative, was synthesized and evaluated as an effective antimitotic agent in our laboratory. However, the molecular mechanisms are uncertain. In this study, HKL-1 was demonstrated to induce multipolar spindles, sustain mitotic arrest and generate multinucleated cells, all of which indicate mitotic catastrophe, in human leukemia HL-60 cells.
View Article and Find Full Text PDFThe renin-angiotensin system exerts a profound regulatory effect on the functional features of dendritic cells (DCs), thus suggesting a new target of angiotensin II (Ang II) action in the immune system. This study analyzed whether peroxisome proliferator-activated receptor-gamma (PPAR-gamma) activation in DCs regulated Ang II-induced activation of DCs and exploited the possible molecular mechanisms, especially focused on the signaling pathways of mitogen-activated protein kinase (MAPK) and nuclear factor-kappa B (NF-kappaB). Ang II stimulation of human monocyte-derived DCs resulted in an intermediate state of DC maturation and function via modulating the balance of the negative or positive regulation of the signaling pathways of extracellular regulated kinase (ERK), p38 MAPK and NF-kappaB, but not c-Jun N-terminal kinase (JNK).
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