Interfacial and thickness effects in La2/3_{2/3}Sr1/3_{1/3}MnO3_3/YBa2_2Cu3_3O7_{7} superlattices

Superlattices of correlated oxides have been used to explore interfacial effects and to achieve additional control over the physical properties of individual constituents. In this work, we present a first-principles perspective of the strain and thickness effects in La$_{2/3}$Sr$_{1/3}$MnO$_3$/YBa$_2$Cu$_3$O$_{7}$ (LSMO/YBCO) superlattices. Our findings indicate that the presence of epitaxial strain and LSMO leads to a reduction of buckling parameters of the interfacial CuO$_2$ planes, as well as the transfer of electrons from LSMO to YBCO. In addition, the change in Cu-3$d$ valence is slightly dependent on the LSMO layer thickness. More interestingly, the in-plane ferromagnetic ground state within the CuO$_2$ planes near the interface is induced due to the local moments centered at the copper atoms. These local moments are decoupled from the charge transfer and, according to our calculations, appear mainly due to the Mn $3d$-O $2p$-Cu $3d$ hybridization being restricted to the interfacial region. The induced net magnetic ordering in interfacial copper atoms may have implications in the control of the superconducting state in the LSMO/YBCO superlattices

Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes

Lens epithelium-derived growth factor (LEDGF/p75) tethers lentiviral preintegration complexes (PICs) to chromatin and is essential for effective HIV-1 replication. LEDGF/p75 interactions with lentiviral integrases are well characterized, but the structural basis for how LEDGF/p75 engages chromatin is unknown. We demonstrate that cellular LEDGF/p75 is tightly bound to mononucleosomes (MNs). Our proteomic experiments indicate that this interaction is direct and not mediated by other cellular factors. We determined the solution structure of LEDGF PWWP and monitored binding to the histone H3 tail containing trimethylated Lys36 (H3K36me3) and DNA by NMR. Results reveal two distinct functional interfaces of LEDGF PWWP: a well-defined hydrophobic cavity, which selectively interacts with the H3K36me3 peptide and adjacent basic surface, which non-specifically binds DNA. LEDGF PWWP exhibits nanomolar binding affinity to purified native MNs, but displays markedly lower affinities for the isolated H3K36me3 peptide and DNA. Furthermore, we show that LEDGF PWWP preferentially and tightly binds to in vitro reconstituted MNs containing a tri-methyl-lysine analogue at position 36 of H3 and not to their unmodified counterparts. We conclude that cooperative binding of the hydrophobic cavity and basic surface to the cognate histone peptide and DNA wrapped in MNs is essential for high-affinity binding to chromatin

A Statistically Rigorous Test for the Identification of Parent−Fragment Pairs in LC-MS Datasets

Untargeted global metabolic profiling by liquid chromato-graphy−mass spectrometry generates numerous signals that are due to unknown compounds and whose identification forms an important challenge. The analysis of metabolite fragmentation patterns, following collision-induced dissociation, provides a valuable tool for identification, but can be severely impeded by close chromatographic coelution of distinct metabolites. We propose a new algorithm for identifying related parent−fragment pairs and for distinguishing these from signals due to unrelated compounds. Unlike existing methods, our approach addresses the problem by means of a hypothesis test that is based on the distribution of the recorded ion counts, and thereby provides a statistically rigorous measure of the uncertainty involved in the classification problem. Because of technological constraints, the test is of primary use at low and intermediate ion counts, above which detector saturation causes substantial bias to the recorded ion count. The validity of the test is demonstrated through its application to pairs of coeluting isotopologues and to known parent−fragment pairs, which results in test statistics consistent with the null distribution. The performance of the test is compared with a commonly used Pearson correlation approach and found to be considerably better (e.g., false positive rate of 6.25%, compared with a value of 50% for the correlation for perfectly coeluting ions). Because the algorithm may be used for the analysis of high-mass compounds in addition to metabolic data, we expect it to facilitate the analysis of fragmentation patterns for a wide range of analytical problems

Altered expression of topoisomerase IIα contributes to cross-resistant to etoposide K562/MX2 cell line by aberrant methylation

KRN 8602 (MX2) is a novel morpholino anthracycline derivative having the chemical structure 3′-deamino-3′-morpholino-13-deoxo-10-hydroxycarminomycin hydrochloride. To investigate the mechanisms of resistance to MX2, we established an MX2-resistant phenotype (K562/MX2) of the human myelogeneous leukaemia cell line (K562/P), by continuously exposing a suspension culture to increasing concentrations of MX2. K562/MX2 cells were more resistant to MX2 than the parent cells, and also showed cross-resistance to etoposide and doxorubicin. Topoisomerase (Topo) IIα protein levels in K562/MX2 cells were lower of those in K562/P cells on immunoblot analysis and decreased expression of Topo IIα mRNA was seen in K562/MX2 cells. Topoisomerase II catalytic activity was also reduced in the nuclear extracts from K562/MX2 cells when compared with K562/P cells. Aberrant methylated CpG of Topo IIα gene was observed in K562/MX2 cells when compared with the parent line on methylation-specific restriction enzyme analysis. To overcome the drug resistance to MX2 and etoposide, we investigated treatment with 5-Aza-2′-deoxycytidine (5AZ), which is a demethylating agent, in K562/MX2 cells. 5-Aza-2′-deoxycytidine treatment increased Topo IIα mRNA expression in K562/MX2 cells, but not in K562/P cells, and increased the cytotoxicity of MX2 and etoposide. Methylated CpG was decreased in K562/MX2 cells after 5AZ treatment. We concluded that the mechanism of drug resistance to MX2 and etoposide in K562/MX2 cells might be the combination of decreased expression of Topo IIα gene and increased methylation, and that 5AZ could prove to be a novel treatment for etoposide-resistant cell lines, such as K562/MX2

Communication With Older Patients With Cancer Using Geriatric Assessment: A Cluster-Randomized Clinical Trial From the National Cancer Institute Community Oncology Research Program

Importance: Older patients with cancer and their caregivers worry about the effects of cancer treatment on aging-related domains (eg, function and cognition). Quality conversations with oncologists about aging-related concerns could improve patient-centered outcomes. A geriatric assessment (GA) can capture evidence-based aging-related conditions associated with poor clinical outcomes (eg, toxic effects) for older patients with cancer. Objective: To determine whether providing a GA summary and GA-guided recommendations to oncologists can improve communication about aging-related concerns. Design, Setting, and Participants: This cluster-randomized clinical trial enrolled 541 participants from 31 community oncology practices within the University of Rochester National Cancer Institute Community Oncology Research Program from October 29, 2014, to April 28, 2017. Patients were aged 70 years or older with an advanced solid malignant tumor or lymphoma who had at least 1 impaired GA domain; patients chose 1 caregiver to participate. The primary outcome was assessed on an intent-to-treat basis. Interventions: Oncology practices were randomized to receive either a tailored GA summary with recommendations for each enrolled patient (intervention) or alerts only for patients meeting criteria for depression or cognitive impairment (usual care). Main Outcomes and Measures: The predetermined primary outcome was patient satisfaction with communication about aging-related concerns (modified Health Care Climate Questionnaire [score range, 0-28; higher scores indicate greater satisfaction]), measured after the first oncology visit after the GA. Secondary outcomes included the number of aging-related concerns discussed during the visit (from content analysis of audiorecordings), quality of life (measured with the Functional Assessment of Cancer Therapy scale for patients and the 12-Item Short Form Health Survey for caregivers), and caregiver satisfaction with communication about aging-related patient concerns. Results: A total of 541 eligible patients (264 women, 276 men, and 1 patient did not provide data; mean [SD] age, 76.6 [5.2] years) and 414 caregivers (310 women, 101 men, and 3 caregivers did not provide data; mean age, 66.5 [12.5] years) were enrolled. Patients in the intervention group were more satisfied after the visit with communication about aging-related concerns (difference in mean score, 1.09 points; 95% CI, 0.05-2.13 points; P = .04); satisfaction with communication about aging-related concerns remained higher in the intervention group over 6 months (difference in mean score, 1.10; 95% CI, 0.04-2.16; P = .04). There were more aging-related conversations in the intervention group’s visits (difference, 3.59; 95% CI, 2.22-4.95; P  Conclusions and Relevance: Including GA in oncology clinical visits for older adults with advanced cancer improves patient-centered and caregiver-centered communication about aging-related concerns. Trial Registration: ClinicalTrials.gov identifier: NCT02107443</p