How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape

The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used 13C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loo

How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape

The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used 13C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loop

Strong Correlation between SHAPE Chemistry and the Generalized NMR Order Parameter ( S 2 ) in RNA

The functions of most RNA molecules are critically dependent on the distinct local dynamics that characterize secondary structure and tertiary interactions and on structural changes that occur upon binding by proteins and small molecule ligands. Measurements of RNA dynamics at nucleotide resolution set the foundation for understanding the roles of individual residues in folding, catalysis, and ligand recognition. In favorable cases, local order in small RNAs can be quantitatively analyzed by NMR in terms of a generalized order parameter, S2. Alternatively, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry measures local nucleotide flexibility in RNAs of any size using structure-sensitive reagents that acylate the 2'-hydroxyl position. In this work, we compare per-residue RNA dynamics, analyzed by both S2 and SHAPE, for three RNAs: the HIV-1 TAR element, the U1A protein binding site, and the Tetrahymena telomerase stem loop 4. We find a very strong correlation between the two measurements: nucleotides with high SHAPE reactivities consistently have low S2 values. We conclude that SHAPE chemistry quantitatively reports local nucleotide dynamics and can be used with confidence to analyze dynamics in large RNAs, RNA-protein complexes, and RNAs in vivo

Peer led post exam review- a paradigm shift in undergraduate nursing education

Traditional approaches in nursing education for students to review exam answers involve a one-on-one interaction between the student and the educator. Students review exam answers and discuss questions with the educator. This may be daunting for many students who are uncomfortable with the traditional instructor-centered paradigm of a one-on-one interaction with educators and therefore may be reluctant to participate, seek feedback and ask relevant questions pertaining to their knowledge. However, this may not provide a supportive and effective learning environment for the student to problem solve and translate knowledge. Increasing student enrollment and faculty shortages are factors that must be considered when developing meaningful strategies for reviewing exam answers. A peer-led post exam review session, using a constructivist learning approach was implemented with second-year course in an undergraduate nursing program within Canada on two separate occasions. Educators facilitated student-centered 20-minute sessions with 12 to 15 students. Each student was provided with their exam answers as well as a copy of the exam answer key. Students were encouraged to be self-directed and actively collaborate with their peers to reflect on their exam answers; identifying areas of strength and growth. Students were allowed to access additional learning resources relevant to the course content. The objective of the session was to create a social learning environment for students that supported peer learning; building their knowledge and capacity to be self-sustainable in their learning. Overall both students and educators found this experiential learning meaningful and supportive.N

Fostering Deeper Learning through Promoting Reflective Practice and Critical Thinking in Undergraduate Students

In this interactive presentation we will engage the audience in discussion of their experiences related to development of reflective practice and critical thinking with their students. In 2010, the Faculty of Nursing implemented a revised undergraduate curriculum that integrated theory and practice in a non-traditional manner, based on a premise that students improve their reflective practice and critical thinking when they explore their learning experiences in facilitated practice-related discussions. The concepts of reflective practice and critical thinking can be ambiguous and may cause educators to feel overwhelmed and thus reluctant to focus on developing these skills with students. Yet, for effective nursing practice, nursing education needs to prepare nurses to address the complexity of the health of the population (Benner, Sutphen, Leonard and Day 2010) including the ability to engage in both reflective practice and critical thinking. Using a constructivist grounded theory approach, we studied the instructors’ understanding of the meaning of reflective practice and critical thinking and the teaching strategies they used to promote the development of these attributes in their students at both the University of Calgary and at Medicine Hat College. We will present the preliminary findings of this study as a basis for the interactive discussion. The intended learning outcomes of the interactive session are for the audience to consider the meaning of critical thinking and reflective practice along with strategies for fostering these attributes in students and discuss how these thoughts resonate with their own definitions and teaching practice.N

Frequency of Somatic TP53 Mutations in Combination with Known Pathogenic Mutations in Colon Adenocarcinoma, Non–Small Cell Lung Carcinoma, and Gliomas as Identified by Next-Generation Sequencing

The tumor suppressor gene TP53 is the most frequently mutated gene in human cancer. It encodes p53, a DNA-binding transcription factor that regulates multiple genes involved in DNA repair, metabolism, cell cycle arrest, apoptosis, and senescence. TP53 is associated with human cancer by mutations that lead to a loss of wild-type p53 function as well as mutations that confer alternate oncogenic functions that enable them to promote invasion, metastasis, proliferation, and cell survival. Identifying the discrete TP53 mutations in tumor cells may help direct therapies that are more effective. In this study, we identified the frequency of individual TP53 mutations in patients with colon adenocarcinoma (48%), non–small cell lung carcinoma (NSCLC) (36%), and glioma/glioblastoma (28%) at our institution using next-generation sequencing. We also identified the occurrence of somatic mutations in numerous actionable genes including BRAF, EGFR, KRAS, IDH1, and PIK3CA that occurred concurrently with these TP53 mutations. Of the 480 tumors examined that contained one or more mutations in the TP53 gene, 219 were colon adenocarcinomas, 215 were NSCLCs, and 46 were gliomas/glioblastomas. Among the patients positive for TP53 mutations diagnosed with colon adenocarcinoma, 50% also showed at least one mutation in pathogenic genes of which 14% were BRAF, 33% were KRAS, and 3% were NRAS. Forty-seven percent of NSCLC patients harboring TP53 mutations also had a mutation in at least one actionable pathogenic variant with the following frequencies: BRAF: 4%, EGFR: 10%, KRAS: 28%, and PIK3CA: 4%. Fifty-two percent of patients diagnosed with glioma/glioblastoma with a positive TP53 mutation had at least one concurrent mutation in a known pathogenic gene of which 9% were CDKN2A, 41% were IDH1, and 11% were PIK3CA

Solid-State Nuclear Magnetic Resonance Spectroscopy Studies of Furanose Ring Dynamics in the DNAHhaI Binding Site

The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5′-GCGC-3′ moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes \u3c 0.3 Å). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5′-GCGC-3′ is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the HhaI methyltransferase

Familienzentrierte Pflege : Lehrbuch für Familien-Assessment und Interventionen

Original Buch: Wright & Leahey’s Nurses and Families (2019). (7. Ed.) Philadelphia: Davis Compan