Investigation of the cis-trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute-solvent interactions and effects of terminal positively charged amino acid residues.

Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74-76 cm-1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm-1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm-1, whereas the PPI has bands at 365, 660, and 960 cm-1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm-1 mode comprising the motion of a C[double bond, length as m-dash]O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio.

A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studies.

BACKGROUND: The frequent recurrence of early-stage non-small-cell lung cancer (NSCLC) is generally attributable to metastatic disease undetected at complete resection. Management of such patients depends on prognostic staging to identify the individuals most likely to have occult disease. We aimed to develop and validate a practical, reliable assay that improves risk stratification compared with conventional staging. METHODS: A 14-gene expression assay that uses quantitative PCR, runs on formalin-fixed paraffin-embedded tissue samples, and differentiates patients with heterogeneous statistical prognoses was developed in a cohort of 361 patients with non-squamous NSCLC resected at the University of California, San Francisco. The assay was then independently validated by the Kaiser Permanente Division of Research in a masked cohort of 433 patients with stage I non-squamous NSCLC resected at Kaiser Permanente Northern California hospitals, and on a cohort of 1006 patients with stage I-III non-squamous NSCLC resected in several leading Chinese cancer centres that are part of the China Clinical Trials Consortium (CCTC). FINDINGS: Kaplan-Meier analysis of the Kaiser validation cohort showed 5 year overall survival of 71·4% (95% CI 60·5-80·0) in low-risk, 58·3% (48·9-66·6) in intermediate-risk, and 49·2% (42·2-55·8) in high-risk patients (p(trend)=0·0003). Similar analysis of the CCTC cohort indicated 5 year overall survivals of 74·1% (66·0-80·6) in low-risk, 57·4% (48·3-65·5) in intermediate-risk, and 44·6% (40·2-48·9) in high-risk patients (p(trend)<0·0001). Multivariate analysis in both cohorts indicated that no standard clinical risk factors could account for, or provide, the prognostic information derived from tumour gene expression. The assay improved prognostic accuracy beyond National Comprehensive Cancer Network criteria for stage I high-risk tumours (p<0·0001), and differentiated low-risk, intermediate-risk, and high-risk patients within all disease stages. INTERPRETATION: Our practical, quantitative-PCR-based assay reliably identified patients with early-stage non-squamous NSCLC at high risk for mortality after surgical resection. FUNDING: UCSF Thoracic Oncology Laboratory and Pinpoint Genomics.

Leukocyte mitochondrial alterations after cardiac surgery involving cardiopulmonary bypass: clinical correlations.

Cardiac surgery with the use of cardiopulmonary bypass (CPB) is known to initiate systemic inflammatory responses that are associated with immune dysregulations, but the pathomechanisms underlying these changes remain elusive. Mitochondrial transmembrane potential (MTP) is an important determinant of leukocytic functions and viability, and may be altered as a part of the cellular responses to systemic inflammatory insults. Therefore, we examined MTP in three subsets of peripheral leukocytes in 18 patients receiving uncomplicated cardiac surgery involving CPB. The MTP of neutrophils and lymphocytes significantly increased, whereas that of monocytes significantly declined, after the surgery. The alterations in leukocytic MTP were transient, normalizing 3 days to 1 week after the surgery, and were accompanied by transient overproduction of intracellular oxidants, including nitric oxide and superoxide. Despite these perturbations, the viability status of leukocytes remained unaltered. Positive correlations were found between the changes of leukocyte MTP and various clinical parameters, implying that leukocyte mitochondrial alterations are parts of the systemic immune perturbations induced by the bypass surgery.